Fortunate Journey Season 1
by ShaViva
Summary: An accidental trip through the Stargate turns out to be fortuitous when a potential weapon to defeat the Wraith is discovered. Told from the 1st person perspective of original char. AU'd Season 1 includes OC plus new ship for Shep. COMPLETE!
1. You need to get out of here – NOW!

**Fortunate Journey**

Author: ShaViva

Rating: M

Content Warning: Some adult themes, minor language, minor violence

Season: 1

Summary: An accidental trip through the Stargate turns out to be fortuitous when a potential weapon to defeat the Wraith is discovered. This is the story of season 1 from the first person perspective of an original character – I have followed the basic sign posts for season 1 but AU'd everything to include my character and a relationship for Sheppard into the mix.

Classifications: Drama, Romance

Pairings: John Sheppard & Original Character

Spoilers for: Everything in Season 1 but especially Hide and Seek, The Storm, The Eye, The Gift, Sanctuary, Before I Sleep, and The Siege Pt 1, 2 and 3.

Disclaimer: The Stargate characters, storylines, etc aren't mine – I'm just taking them out for a little test drive. I am unfortunately not associated in any way with the creators, owners, or producers of Stargate or any of its media franchises. All publicly recognizable characters, settings, equipment, etc are the property of whoever owns them. The original characters and plot and anything else I made up are the property of me, the author. No copyright infringement is intended.

Authors Note: This hasn't been checked by anyone else so any errors are entirely my doing (despite the many many many times I've read and reread it looking for them!). I have basically written the whole story - it's around 35 chapters and I will attempt to put up a new chapter every day or so (depending on how many times I feel I have to reread it before I think it's good enough). Also note that this is the first fan fiction I've ever written and also the first thing I've written that I ever let anyone else read - any constructive comments would be very much appreciated.

And finally, please stick with the story past the first couple of chapters because I have to set the scene for my original character before I put everyone else into it. If you just want to get into the bits based on Season 1 episodes you could skip to Chapter 4.

Copyright (c) 2008 ShaViva

**Chapter 1: You need to get out of here – NOW!**

I know what you're going to say - that it would be impossible for someone to end up in another galaxy by accident. Before it happened to me I would have agreed! I was between jobs and had decided to head down to Cheyenne Mountain in Colorado for no particular reason other than that I'd never been there before and it was a long way so I'd get to do some real driving. That first night I stumbled across a place called O'Malleys - it was pretty busy but I managed to find a seat at the bar.

"Is this seat taken?" I turned to see the voice belonged to a young, good looking guy with a crew cut almost standing to attention beside me.

"No," I admitted in a neutral tone, not wanting to encourage any unwanted attention.

"Greg Evans," he held out a hand to introduce himself.

"Sabina Scott," I replied, shaking his hand quickly before pulling away.

He sat down and before too long we were engaged in amicable conversation. Turns out he was really Private Greg Evans, newly graduated and now stationed at the Cheyenne Mountain Air Force base. Apparently they did deep space radar telemetry there. When I expressed my surprise that he'd be involved in something so ... geeky, he admitted that there were also a number of other "top secret" projects based there and that he was part of one of those.

I was surprised to find I'd been talking to Greg for almost two hours - we'd struck up an easy friendship very quickly, which was handy for me because Greg pointed me in the direction of cheap accommodation and said he'd show me around during his off hours.

I did all the touristy things over the next week or so, based on Greg's recommendations and sometimes with him acting as tour guide. Greg was good company but I could see he was perhaps getting a bit too _fond _of me and I was thinking it might be time to move on again. I wasn't sure if he was just trying to impress me but when Greg offered to take me to see where he worked I jumped at the chance.

"They just let civilians on the base?" I asked in amazement.

"Not exactly," Greg admitted. "There's a big project starting tomorrow and there'll be a lot of civilians around."

"So you can just sign me in?" I persisted.

"Uh ... no," Greg hesitated. "I'd need to get you the right clothes first and ... "

"Is that legal?" I interrupted. "I don't want you to get in trouble."

"It'll be so busy no one will be any the wiser," Greg said confidently. "If anyone asks I'll just tell them you're someone else and get you out of there before they can check to confirm it. It'll be a piece of cake."

I can't believe that I agreed to a plan that clearly had so many holes, but the next day I found myself dressed in a uniform that looked anything but military, milling around in the foyer of NORAD with a whole bunch of other people dressed very similarly. Some of them were clearly foreign as there were a lot of conversations going on around me that I couldn't understand a word of. Turns out part of Greg's job was signing people in, issuing visitors passes, and escorting them around the base. No wonder he'd been so confident he could smuggle me in and out without detection!

Greg had pointed out that I'd have to pretend I didn't know him and recommended I stay in the middle of the group so there'd be less chance that I'd draw attention to myself. The plan was I'd follow with the group until Greg had escorted them to a briefing room down on level 28 at which time I'd hang back and he'd then take me for a quick tour before getting me back up to the surface.

Everything went according to plan - we made it to level 28 and through the final check point with no problems, and headed down a long concrete corridor towards the briefing room. That's when things started to go wrong - Greg was called back to his post upstairs to bring down a couple of civilians who'd been running late. I exchanged a pointed glance with him and he just motioned for me to go with the flow until he got back. Great, I thought, sitting at the back of the room and slouching down in my seat.

I barely listened to the guy at the front who was talking about their mission and how they had to all carry their own pack and as many other supplies as they could handle through the gate. There were a few other comments about safety and obeying the orders of the military before the briefing closed and everyone started getting up. Greg still wasn't back and I didn't know what else to do except follow along with everyone else. We proceeded down the corridor and when we turned a corner I was confronted with the sight of fifty or so people milling in groups of a similar size to my own. There were also metal cases, probably containing those supplies they'd talked about, stacked along one side of the corridor and hiking packs resting against the walls. A military guy stood at doors leading into a room I couldn't see and was motioning each group through at a steady pace - they'd pick up their packs and some boxes before disappearing through the doors. I did wonder briefly how it was possible to leave for a mission when we were 28 floors below the surface but my worry at being caught where I wasn't meant to be was taking up most of my active consciousness.

When it was my groups turn to head through those doors I looked desperately back down the corridor hoping that Greg would appear and get me out of this. He'd told me up front that under no circumstances should I admit to anyone that I didn't have real clearance to be there - I was peeved that he'd gotten me into this mess and that his plan had gone so badly but I didn't want to get him (or _myself_) into trouble so I stuck to that. Realising he wasn't going to appear any time soon I just followed my group through those doors, hoping I'd come up with something before it was too late.

We entered a very large room dominated by a metal ramp leading up to a really really really big circular device that was suspended at the end of the ramp by huge clamps coming out of the floor and walls. The most amazing thing was that the inside of the device enclosed a blue sparkly substance that looked like a puddle of water. I watched as the group before mine walked up the ramp and then straight through the puddle– there was no room behind the ramp so it was as if they'd just vanished into thin air. I could feel a horrible rush of panic sweeping over me as my brain tried to process the impossible sight I'd just witnessed.

"You need to get out of here ... NOW!!" that little voice in my head that we all have was yelling at me. I turned against the mass of people heading for the puddle and spotted the military guys with BIG guns in the corners of the room. Did I really want to be arrested for being somewhere I was clearly not meant to be?

Greg would work out what had happened and find a way to get me out of this - I knew I'd be held accountable too because there was no way I could deny I'd known he was doing the wrong thing. I really should have checked before coming here what the penalty was for running around a military base without proper clearance. Because I didn't know how serious that might be I decided in my panicked state that my best move would be to just keep going with the flow. Whatever was on the other side of that puddle seemed much more attractive at that point than a concrete prison cell inside this mountain.

So I just followed along in the middle of all the people, holding tight to the boxes I'd picked up before I entered the room, and walked up the ramp. Up close I could almost feel the energy being emitted from the puddle – it really was a spectacular sight I would have liked to study more but the mass of people moving behind me pushed me forward and I stepped through.

No words I have at my disposal could describe the sensation of being drawn into the puddle, nor the disorientation I felt moments later when I stepped out into an even huger room than I had just left. I looked around me and could see nothing familiar about where I was – how was it possible for me to arrive somewhere so far removed from where I had just left?

The mass of people carried me along out of the range of the puddle still glowing behind me, casting much needed light over the darkened room. A military guy who was clearly in charge was directing people to find a place to put down their burdens and wait until everyone had arrived through the "gate". I'd heard that same reference in the briefing room - was that what they called the puddle thing?

I looked around in amazement. Directly ahead of the gate was a flight of steps leading up to another floor with balconies that overlooked the gate room. I could see people up there looking at consoles and gesturing excitedly. Without meaning to I made eye contact with another military guy standing on the balcony looking down at the gate room – this one had dark messy hair and an expression that made me think that he too was wondering where the hell he was and why he thought it had been a good idea to step through that puddle. He was looking at me and I was looking at him ... to be honest thinking how hot he was ... I know! How could I be thinking that when I was god knows where in what was clearly a heap of trouble caused by another guy I'd also thought was cute? Then I remembered where I was and after giving a small nervous smile I broke eye contact and turned to find a spot somewhere out the way – very far out the way - so I could figure this all out.

People were still stepping through the gate and all attention seemed to be on directing the new comers so I just kept walking down a corridor with my boxes in tow until I couldn't hear the sounds of excited voices anymore. I found a door and it opened as I approached. The lights came on automatically which I thought was kind of cool but also very worrying if someone noticed. The lights dimmed again once I was inside with the door closed behind me. There was just enough light for me to see that I was in some kind of personal quarters with a bed and everything. I put down the boxes and collapsed onto the bed, dropping my head tiredly into my hands. What was I going to do now?

I hadn't slept the previous night because I'd been so nervous about sneaking onto a military base. Either that or my trip through the "gate" had taken more out of me than I realised. In any case, a huge wave of tiredness swept over me and I flopped myself down fully onto the bed – it was very comfortable so it didn't take much for me to drop off to sleep. My last thought before sleep overtook me was the desperate hope that no one would discover my hiding place before I woke up.

I didn't know where I was at the time but that's how I ended up on Atlantis in a whole other galaxy.


	2. Aren't you forgetting something?

**Chapter 2: Aren't you forgetting something?**

The shaking of the city woke me some time later – after a few moments the tremors stopped and I relaxed back onto the bed. I had the sense that I'd been asleep for a long time and at first I had no idea where I was. It was quiet and dark and actually pretty creepy waking up in that strange room. The lights came on a little and I scanned the room as my brain filled in the gaps and reminded me I was as lost as any person had ever been. And pretty damn hungry too. I didn't really have any plan in mind about how I was going to get out of the mess I had gotten into – all I knew was that I didn't want to get caught and tossed into jail which seemed like the only outcome I could imagine now that things had gone so far.

So food – how was I going to deal with that if my intention was to hide? I searched the boxes I'd carried through the gate and found a bunch of electrical components that might have been useful to someone else but not to me. Looking in my bag I discovered the bottle of water and package of nuts I'd put in there the morning this whole mess had started. Realising that there was no point in rationing such a meagre set of supplies, I decided to assuage my hunger and worry about my next meal later.

After eating I explored my little room some more and discovered that I had another door leading out onto a little balcony. It opened automatically as I approached (how cool was that!) and I got my first very worrying sight of where I was. All I could see was water ... lots and lots and lots of water. So – no chance of escaping and finding my way home out _that_ door. My heart was beating super fast and I felt that horrible wash of sensation come over me that you only get when you think about something really scary. I sat down right where I was and put my head on my knees, breathing deeply. I had expected to see mountainside because that's what I'd seen just before I entered the NORAD base. A big ocean of water was as far as you could get from that. Was I in some other country completely and how had that happened and more importantly how was I going to get home now?

Not knowing what else to do, I decided my only priorities right then should be survival and NOT getting caught. The room had bathroom facilities so that wasn't going to be a problem. Although my desire to remain hidden would give me the motivation to go as long as possible without food I knew within a day or two I'd have to go in search of supplies.

You know how in movies when someone stows away and is then discovered they emerge from their tiny box or whatever they've been hiding in showing little sign that it was even a hardship? So not the case in reality! After only one day in my spacious (especially compared to a box) hiding place with absolutely nothing to do I began to feel very frustrated. The fact that I didn't know anything about what was going on outside my room was driving me nuts and I decided that that night I'd risk it and try to find some supplies as well as a little more about where I was.

I say "night" because although I'd been using my watch to determine how much time had gone by I couldn't reconcile night and day – when my watch said it should be midnight it was blazing with light outside on my balcony so either there was something wrong with my watch or I was in a completely different time zone.

The waiting for darkness was killing me – seriously I hate waiting for anything in general and this was worse because at the back of my mind I was coming up with various ways I could explain my presence when I got caught by the very scary looking military guys I was sure would be jumping me as soon as I opened my door.

Luckily all that worrying was for nothing because when I peeked out my door no one was there. Hoping that no one would find my room while I was gone I checked to make sure the door did close automatically after me (still cool – like being on Star Trek without the people with pointy ears) before creeping off down the corridor.

I decided to head in the opposite direction I'd come from to avoid the whole gate area that I assumed would be busy no matter what time of the day it was. I heard voices from down the corridor and quickly ducked into a side passage to wait for them to pass. And that's when I had my truly great idea – it had only been a couple of days – would everyone really know who everyone else was? Maybe I could hide out _in plain sight_ instead of creeping around and looking suspicious. It was late so the number of people around would be small and as long as I behaved as though I _belonged_ here I could totally get away with it.

Taking a deep breath and trying to put on an expression of serious belongingness I stepped out of my hiding spot. I tried to imprint on my memory enough markers so I could find my way back again before I walked confidently down the corridor, following those voices I had heard previously.

The voices led me to an area that was clearly some kind of commissary – it looked like they only had military rations but I couldn't afford to be fussy. I grabbed a tray like the two guys I'd followed and continued to emulate them as I picked up a packaged meal, a coffee (yeah – caffeine!) and a bottle of water to take back to my room. I sat a few tables away from my "tour guides" and bent my head down, trying not to rush the first meal I'd had since arriving here. Once done I sat for some more thinking about my next move and frankly being surprised that I was still "at large". That's when it happened ... I spotted that military guy I'd admired my first few minutes here. And he was looking right at me with a puzzled look on his face ... I knew he was trying to remember where he'd seen me before.

"Oh _crap_" I thought. "He's coming over ... what do I do? What do I _do_!"

Pasting a weak smile on my face I looked up when he stopped in front of me and said Hi.

"Hello," I replied. Geez, could I sound any more nervous?

"I don't know your name," he said "but I remember seeing you when we first got to Atlantis."

"Yeah – been pretty busy since then," I said, trying to sound like I had a purpose, other than trying not to pass out because I'd suddenly forgotten how to breathe.

"Major John Sheppard," he introduced himself, holding out his hand.

"Nice to meet you," I replied, shaking his hand and then quickly letting it go when I felt a not altogether unpleasant jolt pass from his hand to mine. "Sorry to rush off but I really have to get back to my ... work," I added, gathering up my tray as I pushed my chair back and away from him.

"Aren't you forgetting something?" he asked.

I turned back to look at him ... noticing again how seriously hot he was especially now that I could see he had these deep hazel coloured eyes and a quirky grin on his face – did I do something amusing?

"What?" I asked. That came out sharper than I'd intented but I seriously wanted to get out of there and I didn't know what I was going to say if he asked me for my name. Should I tell the truth or just make something up?

"Your laptop," he said, pointing to the computer I hadn't noticed was sitting on the table when I'd sat down.

I smiled again in thanks, grabbed it quickly, and then make a hasty exit. I turned to look back once I'd got to the entrance and saw he was still standing at my table watching my retreat with that same puzzled look on his face.

Once back in my room I sat on the bed breathing deeply. It had been a very nerve racking experience but well worth it. I now knew I was in a place called Atlantis – the very name of which sent a chill mix of dread and excitement through me. And I had a laptop which even if it didn't contain more information would at the very least have games (please not just solitaire – I hate that game) to relieve my boredom.


	3. This was a one way mission

**Chapter 3: This was a one way mission.**

I know what you're thinking – sure I had a laptop but I didn't have a password so I wouldn't be able to use it. And I still had to risk more trips from my room because I had stupidly forgotten to grab anything more than the water in my haste to escape from the Major.

It just so happens that I have a particular talent for computers. Trying to crack someone's password is pretty difficult given the number of possible combinations and not knowing anything about whoever's laptop this was. But you don't have to actually do that – I got myself access to the laptops base code and set myself up as an administrator to bypass the old user and to give myself access to everything. Within a couple of hours I had full use of the laptop which contained a lot of information about an expedition to Atlantis.

I could hardly believe what I was reading – was the owner of this laptop a fiction writer in their spare time? If not then I was clearly in the twilight zone because apparently the gate I heard referenced my first day here was actually called a Stargate and it was a portal for interplanetary (or in our case intergalactic) travel between planets through means of a stable wormhole.

CRAP!

Earth had enemies – parasitic beings bent on domination of all lesser species like us. I lived on Earth and had never thought of it as "Earth" before so that was hard enough to grasp let alone the whole idea of scary alien enemies. The expedition to Atlantis was partly to search for weapons or technology to defeat this enemy.

That's when I discovered the worst part. This was a one way mission. We were so far away from Earth as to make any hope of returning without the Stargate impossible. They'd used something called a ZPM to power the Earth gate but didn't have sufficient power to do the same with the Atlantis gate. I was stuck here forever!

Again that same horrible wash of "I am scared witless and in danger of a serious panic attack" sensations overcame me and I sank down on my bed to concentrate on the suddenly difficult task of breathing properly.

After I don't know how long I got up again and went back to the laptop to see if there were any maps of Atlantis on it or any other information I could use. Clearly I needed a new strategy because the idea of giving myself up was even less appealing now I knew my jail cell wouldn't be a concrete one under a nice mountain but an alien one a million light years away from my home.

I read about a race we called the Ancients. Apparently they had evolved in our galaxy millions of years ago. The Ancients were the gate builders – seeding the Milky Way with Stargates so they could travel easily between planets. There was some kind of plague or something else happened that prompted them to leave our galaxy, taking their city with them. This all happened between 5 and 10 million years ago, after which we became the second evolution of humanity in our galaxy. The Ancients came to this galaxy, which we called Pegasus, and did much the same thing – seeding life throughout the galaxy and putting Stargates everywhere so they could travel easily.

Wanting to know more I kept searching and managed to hack into a sort of intranet I guess – mission reports and other official looking documents – which I could use to find out what was going on right now. That's where I discovered that scary alien enemies back on Earth and being stuck here forever was not the worst news I could discover. That's when I found out about the Wraith who rather than seeing me as an enemy would only see me as a possibly tasty appetiser in a big human banquet.

DOUBLE CRAP!

The Wraith were an enemy so powerful that even the Ancients had been unable to defeat them. Rather than see their city fall to the Wraith they submerged it beneath the sea and retreated back to our galaxy.

After reading all about the rising of Atlantis (apparently I slept through that one) and Major Sheppard waking the Wraith on practically the first day we were here I realised there was no way I could hide in this room forever. It was now not a matter of if I were caught but when and how I was going to take some control of the situation. Still, I could probably get away with at least one more in plain sight exploration and maybe I could find a way to give myself up but not end up in the brig.

I used the laptop some more to try to find out about the people who would leave their homes behind knowing up front that they probably would not be returning. Although I couldn't find things like personnel files or such I did find out enough to know that these people really were "the best of the best" in their fields. I _so_ did not belong here since the closest I've even gotten to being the "best" at anything was the time I had briefly been number one on the Bejeweled 2 Xbox 360 leaderboard! I'm guessing that a talent for matching little coloured shapes was not going to be of much use in Atlantis.

I realised that Major Sheppard would probably be suspicious that I hadn't given him my name, especially if he found out the laptop he gave me wasn't mine and was now missing. I planned my next outing for that night, hoping that Major Sheppard wasn't already looking for me.


	4. I think you're gonna need a bigger boat

**Chapter 4: ****I think you're gonna need a bigger boat****.**

I've read that just before danger is about to descend people often sense it – part of that primordial survival of the species stuff. Sadly I was obviously too far removed from those prehistoric roots because I didn't sense anything. In my defence though I had been dreading and expecting danger since I realised how bad my situation was so how was I supposed to sense the specific danger I was about to face?

I made my way to the commissary much as I had before. This time the room was empty which did make me pause to start with but I just thought maybe there was something going on elsewhere and that's where everyone was. I was just about to enjoy a BIG mug of coffee when the power went out and I was left sitting in complete darkness.

_"Don't panic"_ I coached myself. _"It's an alien city – maybe someone flicked the master switch without realising it."_

After a few minutes with still no power I decided my best course of action would be to return to my room as quickly as I could. I'm not sure how but I ended up in the wrong corridor with no idea how to get back. I walked down the hall, checking each room I came to for something familiar. Glancing into the last room I was startled to see Major Sheppard standing in front of a strange looking device.

"Oh sorry," I stammered, quickly turning around to escape once I'd noticed the incredulous look on his face.

It hardly seemed possible but when I turned to head back down the corridor I discovered that there was something darker than the complete blackness of an Atlantis corridor devoid of light. That darkness was creeping towards me at an alarming rate.

"_RUN_," that little voice in my head screamed.

"Don't move," a too familiar voice whispered in my ear.

I turned my head slowly to see the intent face of Major Sheppard. Looking more closely I realised I was seeing his military persona in full works. He was kitted out in a black vest with lots of pockets and carrying a seriously scary looking weapon. Motioning me behind him he raised that weapon and pointed it at the darkness.

"Get behind me," he commanded. Without even thinking I obeyed that command – so not my usual way as I hate being told what to do without explanation.

"It's too late to get you back to a safe area," Major Sheppard told me in a grim voice. "That thing will be here any second so you need to do exactly what I say."

Without even waiting for my reply he motioned for me to stand as far away from the device as I could get.

"Okay Major. Go ahead," a female voice came from the Major's radio.

Major Sheppard flipped a switch on the device before taking up a position facing the doorway.

Suddenly the lights went off. Being in the dark set off a deep fear inside me that was only slightly lessened when Major Sheppard switched on the light attached to his rifle. The seconds ticked by with neither of us moving. Major Sheppard raised his rifle – looking towards the door I saw that the cloud of darkness had started to ooze its way inside the room.

"It's coming," Major Sheppard reported. "I think you're gonna need a bigger boat."

"Size doesn't matter," a different, male voice responded.

"That's a myth," Major Sheppard quipped.

"It'll fit" that same male voice returned. "The device traps the creature in subspace. You just need to make sure it gets all the way inside the containment vessel."

I had no idea what they were talking about. Luckily the Major seemed to have forgotten I was even there – hopefully I would be just as invisible to whatever that dark cloud was. Major Sheppard backed away as the entity made its way further into the room.

"Alright, come on," Major Sheppard challenged.

The entity reached the device, its mass filling up half the room. It seemed to pause like it was checking out the device, and Major Sheppard standing behind it. A huge sense of relief came over me as I realised the entity was beginning to retreat from the room. Within seconds it had disappeared.

"Son of a bitch!" Major Sheppard cursed. Perhaps the entity leaving wasn't a good thing after all.

"What happened?" the woman's voice came over the radio this time.

"Damned thing took one look and went away," Major Sheppard reported in annoyance. "It's a lot smarter than we thought."

Something must have been said in reply but it didn't register with me because that was the moment when I realised I was no longer invisible and that all of the Majors "military" attention was fully engaged on me.

"WHAT DID YOU THINK YOU WERE DOING?" he yelled (yes yelled – made me jump too because even though he looked seriously pissed off I wasn't expecting that.) "That thing almost killed Lieutenant Ford and you're just wandering down the corridors?"

At this point he was right up in my face and I felt a strange heat flush through my body. Who knew that being yelled at could be so ... arousing. God did I just think that? Get a grip girl!

"Didn't you hear the announcement about staying in quarters?" he asked at a slightly lower volume.

"No," I replied in a very small voice that I'm not sure he even heard. Although he had found me where I was clearly not supposed to be he still hadn't realised that I was in fact not supposed to be anywhere on Atlantis. I was so dead.

"Dr Weir is probably going to ream you out as well," he said. "We've still got to do something about the entity though so for now I'll have to escort you to your quarters where you _will_ wait until you hear otherwise."

"Oh that's not necessary," I said quickly. "I can find my own way to my quarters." That was clearly the wrong thing to say because I could see his anger starting to resurface, as well as see the suspicion in his eyes.

"Listen ..." Major Sheppard began and I could tell that was the point at which he realised he didn't know who the hell I was.

"Who the hell are you anyway?" he demanded.

_"Crap, crap, crap,"_ was all I could think as I looked up at him in misery without answering.

"I don't have time for this right now," he growled, grabbing me around my upper arm and giving me a small shake. "Just tell me who you are or I will throw you in the brig until this whole entity thing is resolved."

But still I couldn't seem to make my vocal chords work and so with a look of utter frustration he dragged me out of the room to a small closet looking thing and shoved me in ahead of him. Touching the screen in front of us made a white light appear and when we stepped out we were in another, different corridor.

_"Transporters"_ I thought giddily. _"This really is like Star Trek."_

Stumbling along after the Major I ended up being dragged not to the brig as I had expected but towards that room I had noticed above the Stargate the day I arrived.

"Dr Weir will sort this out," he growled again, at which point I dug in my heels and tried to pull my arm out of his grasp. I say try because he was seriously strong.

"Don't," I pleaded, pulling on my arm again without success. "Put me in the brig ... I deserve it ... I'm no one ... seriously." I knew I was jabbering at this point but the voice I couldn't find before suddenly wouldn't be silenced. "I can wait until everything is ... fixed ... just don't take me in there with all those people!"

Major Sheppard looked at me closely, clearly weighing up his options. "Since you won't tell me your name or where your quarters are you leave me no choice."

And that's how I ended up in the brig of Atlantis.


	5. And you are?

**Chapter 5: And you are?**

So – the brig in Atlantis. Actually not as scary as I imagine an Earth jail would be. I was in a sort of cage within a big room. I had tried to touch the bars of the cage but got a nasty shock for my pleasure and made sure to stay well clear after that.

This was not how I was hoping things would go when I gave myself up. Not that almost getting ambushed by a big black ... thing ... and having to be saved can be counted as giving oneself up. I was in so much trouble that I just couldn't see how this was going to end any other way but very badly. Realising that it was still night I settled on the bed and tried to get some sleep.

It took a while the next morning before anyone came to check on me – I suppose they were all off getting rid of the black shadow thing. After what seemed like days but was probably only hours I heard the sound of the door opening and looked up to see Major Sheppard enter the room. He still had his I'm seriously pissed off look on so I knew I was in for a bad time.

He stood as close to the bars as he could get without shocking himself and just looked at me for a few moments with a thoughtful look on his face.

"So, let's start again," he said. "I'm Major John Sheppard, the ranking military officer of this expedition. And you are?"

_"Ranking military officer?"_ that voice in my head squeaked. _"You had to go and get caught by the guy in charge!"_ Suddenly I was very nervous and once again my vocal chords just ceased up.

"Look, there's no point in not answering," he said irritably. "I _will_ find out who you are but it'll go better for you if you save me the effort and just cooperate!"

"I don't know what to say," I whispered in misery. "I can tell you my name but it won't mean anything."

"Why the hell not?" Sheppard shot back at me.

"Because I'm no one and I'm not supposed to be here. Not just here in this cell, but here ... on Atlantis ... at all. It's all just a huge mistake!" I said. And then I'm ashamed to say I started crying. Not just dainty little tears either but big fat ones accompanied with that horrible crying sound you make when you're really really upset about something.

"Don't," he pleaded, holding up a hand as if that would stop me. "Please don't do that. I'll go get Dr Weir – she'll sort this out."

"NO!" I shouted. Even though I was scared I still preferred talking to him rather than some other person I'd never met and who didn't know me. Not that he exactly knew me but at least he was familiar with me.

And that's when I told him the whole thing. He was not impressed to say the least. In fact he yelled at me some more – all those things I'd been expecting about infiltrating a military base, stealing uniforms and supplies, and of course stowing away on a mission to another galaxy. The worst bit was when he asked me how I could possibly be so stupid as to step through the Stargate with no idea of what it even was. Stupid – that was me all right.

And then he just turned around and left! Seriously – without saying anything about what would be happening to me. It was only after I'd calmed down a bit that I realised I still hadn't told him my name. The break did me good though because it gave me time to work out that I was actually relieved to have been caught – being "on the run" was a lot more stressful than I would have guess. By the time he came back a little later I felt almost calm.

This time he brought a woman with him who I could only guess was the Dr Weir he'd mentioned previously.

"Hello," she said almost gently. "I'm Dr Elizabeth Weir. Major Sheppard neglected to get your name."

"Sabina," I said reluctantly. "Sabina Scott".

"Well, Sabina," Dr Weir said. "Could you tell me more about how you were able to hide on Atlantis for so long without detection?"

Although I was puzzled by her question I tried to answer it as honestly as I knew how. "I found a room the first day we were here and I just stayed. I didn't do anything special to hide – the room just seemed to do it for me."

"The room 'did it for you'?" this time Major Sheppard questioned me.

"I guess," I replied. "I didn't notice it at first but after a while I realised that when I wanted the lights to go dim they did, just like the doors always opened automatically when I approached – seriously cool by the way."

The small smile I saw Major Sheppard trying to hide encouraged me to go on. "To be honest I didn't think anything of it – I just assumed it was Atlantis doing what it's supposed to do."

"Doors opening automatically – yes. Lights coming on by themselves – yes. Rooms 'hiding' you inside them – not so much." Major Sheppard told me as he exchanged a glance with Dr Weir.

"Oh," I replied is a small voice. "Is that a problem?" I asked nervously. What was that glance all about – had I done something wrong?

"No," Dr Weir replied. "It's just a little unusual is all – so far only a handful of people have been able to operate things in Atlantis the way you've described. We should do a few tests but it's not a big deal. Now about your being on Atlantis - I can understand how you were carried along by the circumstances and ended up here. You should have revealed yourself straight away but I'm happy for Major Sheppard to apply whatever punishment he deems fit – given that the whole idea of a stowaway clearly fits into the definition of a military situation."

I looked at the Major apprehensively. "Punishment?" I asked.

Before Major Sheppard could reply Dr Weir added "You will report to Dr Beckett in the infirmary for a full series of tests with which you will _fully_ cooperate," she ordered. "Once all that's done we'll work out what your place will be here on Atlantis."

"Thank you," I smiled gratefully. It felt like a huge weight had been lifted off my chest. That is until I turned back to glance at Major Sheppard and saw the look on his face. Dr Weir said her goodbyes and left me alone with the still silent Major Sheppard.

"So, " I said feeling just a little more confident now that I knew Dr Weir was not opposed to finding me a place on Atlantis. "What's my punishment going to be?"

Major Sheppard glared at me for a few more moments before turning away, obviously still thinking about it. He waved his hand over a panel and the cell door opened. Instead of letting me out he entered the cell and did a bit more pacing before stopping in front of me.

"I'm pissed at you," he stated. "Three times you had the chance to come clean with me and three times you chose not to. Now while I can understand some of your reasoning, dishonesty and a lack of trust have no place on a mission like this."

"Wait a minute," I interrupted. "I never lied to you!"

"_Don't interrupt me!_" he did that whole command thing with his voice and I just shut right up. "As I said a lack of _trust_ is a serious issue on a mission like this. I need to know that everyone will do what they're told in an emergency situation without having to have things explained to them first. "

He glanced at me to see if I was going to interrupt again and when I remained silent he gave a little nod and then continued. "So your punishment," he almost smiled evilly before delivering my sentence. "will be to undertake _all_ the military training expected of an entry level member of one of my teams as well as any other training Dr Weir sees as essential for members of her teams. You will also help out in any capacity we see fit _without_ question or complaint. Agreed?"

I nodded without comment, looking anywhere but at him. I didn't want him to see the glee in my eyes as I realised I would have the chance to participate and learn more than I'd ever dreamed possible. I knew I wasn't going to be anywhere near as smart as everyone else on Atlantis but right then that didn't even seem to matter.

"First lesson Sabina Scott," Major Sheppard had somehow gotten back into my face and the look he gave me said he was still pissed at me. "For the duration of your time in basic training you will be under my command. When I ask a question you answer it promptly and finish with a Sir – are we clear?"

"Yes ... Sir?" I replied hesitantly.

Major Sheppard frowned before asking me again if I agreed to the terms of my punishment. I looked up with a grin I just couldn't hold in and said in a sing song voice "Yes Sir".


	6. How much running have you done?

**Chapter 6: How much running have you done?**

Things were finally looking up. After Major Sheppard had assigned me some real quarters (remarkably similar to the ones I'd already been living in but sadly without the balcony) he got someone to show me around. Atlantis truly was the most amazing place. Design and technology so obviously alien to anything I'd ever seen before. Stylish and somehow beautiful while still being functional. By the time I begged off to return to my quarters for some sleep I was simply overwhelmed – it was almost more than my brain could take in. Needless to say I fell into a deep sleep and didn't awaken until I heard a beeping sound.

I lifted my heavy head from the pillow and squinted around looking for the source of the beeping. Oh ... right ... the door. I dragged myself off the bed and stumbled to the door still half asleep. Nothing happened when I got there though – where was my automatic door opener?

"WHO IS IT?" I yelled.

"Major Sheppard," came the disgustingly cheerful reply. "Time for your first training session!"

"THE DOOR ISN'T OPENING," I was yelling again.

"Swipe your hand over that panel near the door," Major Sheppard replied with what sounded like a chuckle.

"Oh," I said, doing said swiping. How was I supposed to know the door did that?

The door opened and there on the other side was Major Sheppard looking very alert and frankly way too attractive for that time of the day, speaking of which ...

"What time is it?" I demanded looking for my watch, a pointless habit because Earth time had no meaning there and I still had no idea how they were running all of that.

"6:00am" Major Sheppard replied, looking me up and down and reminding me that I was dressed in a long t-shirt and not much else since the only personal things I had were the clothes I'd borrowed back on Earth.

"I figured you wouldn't have anything to train in so I got you these," the Major held out a pile of clothes which I automatically took. "Sorry if the sizes are wrong – I had to guess. You can requisition whatever else you need from supplies. Five minutes Sabina – get moving!"

The door closed while I contemplated the personal implications of Major Sheppard picking out clothes for me before I shook myself and ran into the bathroom to tidy myself up.

Six minutes later I stepped up to the door which did open automatically this time to reveal Major Sheppard pacing around outside. He glanced at his watch but otherwise didn't comment.

"How much running have you done Sabina?" he asked me.

How could I make none sound any less pathetic than it was? Nothing came to me and I looked at the floor as I mumbled "None".

"I didn't hear you," Sheppard barked the comment.

I looked up quickly to see he was deadly serious. "None, Sir" I replied.

"Well, you won't be saying that again. We'll start out slow ... try to keep up."

And with that he took off. Slow did he say? I didn't think so unless full out sprinting could be considered slow. Before I'd gone 50 metres I was puffing and sweating. Before I'd gone 100 metres I was cursing Major Sheppard for the bastard I knew he was because he was clearly enjoying my suffering. How had I ever considered him attractive? At 6:00am with sweat dripping into my eyes as I chased his smug back up the corridor I was starting to revise that opinion.

Finally the torture was over and after escorting me back to my quarters so I could attempt to recover (my face was still red an hour later!) Major Sheppard took me to the infirmary to begin all those tests Dr Weir had mentioned.

"This is Dr Carson Beckett," Sheppard introduced us. "Do what he says. I'll see you the same time tomorrow morning."

"I am _so_ looking forward to that," I mumbled under my breathe.

"What was that?" I looked up to see Major Sheppard hadn't actually left as I'd supposed.

"Nothing, Sir" I said with a cheeky grin. Shaking his head Sheppard left me to Dr Beckett.

"Let's get started Lass," Dr Beckett said with a friendly smile and a lovely lilting Scottish accent. Now he was attractive and clearly not the type to enjoy other peoples suffering like someone else I was no longer going to think about.

The relief of finally talking to someone who seemed to be pleased to meet me almost brought tears to my eyes. "What do I have to do?" I asked a bit nervously.

"Nothing to worry about," he replied. "We'll start with some basic medical questions, then some blood tests and while we wait for those results there are some written tests I want you to do. It's all pretty easy – just be yourself."

Dr Beckett started out with some basic questions.

"Age?"

"I'm a 29 year old Sagittarius who likes long night walks on the beach and ... yes I _am_ taking this seriously!"

"Height?"

" 177cm (I know – on the tall side for a girl)"

"Hair?"

"Yes – long and painfully straight. Oh sorry – brown. In fact if the answer is a colour just put me down for brown."

"Weight?"

"Is that really necessary? Oh all right! I was 70kg but with my lovely diet of practically nothing for the last few days who knows!" After a proper weigh in I found out that I had lost 5 kilos and was instructed that I should eat more than usual until I'd gotten back to a healthy weight range.

"Illnesses?"

"None that I know of but it's early in the day and I _am_ on a strange planet light years from Earth so who really knows!"

My whole family history was collected and then it was time for me to have some blood extracted. I realised as Dr Beckett prepped my arm for the blood test that he hadn't actually touched me up until that point. I only noticed it then because when he did I felt a slight electric jolt at his touch - no where near as powerful as the one I'd felt with Major Sheppard, but puzzling just the same. Dr Beckett turned back to me with the needle and I shivered just a bit – do needles really have to be that pointy and glinty? Why hadn't he found some kind of Atlantean instrument that could take your blood without sticking a pointy piece of metal in you?

I had no idea there were so many tests they could give me. It literally took hours – I had to have lunch there and we still weren't done. Apart from the medical tests (scans etc) there were personality tests where Dr Beckett would ask things like "What does that black blob look like to you?" and I would reply "You mean apart from a big black blob?" There was even an IQ test – Dr Beckett didn't call it that but I couldn't see what else it could be. I was mega apprehensive about that one as I didn't really want to know how much less intelligent I was than everyone else on Atlantis.

"These results are confidential aren't they?" I asked Dr Beckett, rather casually I thought.

"Of course," Dr Beckett replied. My relief was short lived though when he admitted that Dr Weir and Major Sheppard would of course be informed of all the results so they could find the best place for me. Damn!

The blood test results also seemed to cause a little bit of concern. Dr Beckett took the printout from one of the nurses and his eyebrows shot up as he read the results and not in a good way I thought.

"What's wrong?" I asked

"Oh nothing lass," Dr Beckett replied lightly, still looking worried to me. "One of the things we looked for in staff for Atlantis was what I call the ATA gene – the Ancient Technology Activation gene. We think the Ancients used the gene as a sort of genetic key so that only their kind could operate their technology. Some things require the user to actually have the gene, others only require the gene for the first initialisation, after which anyone can use them. It's really quite rare actually so I was just surprised to see that you have it."

"I have an ancient gene?" I asked. "How is that possible?"

"We don't know why some people have it and some don't. There also appears to be varying degrees of strength to the gene too because for example Major Sheppard is very proficient at operating the ancient technology while yours truly can barely get anything to work."

"So Major Sheppard has the gene too?" I asked. If he had it then it couldn't be that bad. He had been put in charge of the military side after all and they wouldn't have done that if there was something wrong with him.

"Aye lass, as do I. So there you go – nothing to worry about." With a smile he turned back to my blood test results. "Your blood type is O negative which is handy too if you'd be willing to donate blood every now and then." I nodded without replying, still thinking about that ATA gene thing. Was that why the room had hidden me – because I had the gene and Atlantis had somehow recognised that? I wasn't sure whether that made me happy or really really nervous.

The rest of my tests passed without incident and Dr Becket released me for my chat with Dr Weir. I then spent an hour listening to her talk about the history of the Stargate program and Atlantis. Some of it I already knew from my stolen ... sorry _borrowed_ ... laptop but I didn't want to admit that because then I'd have to admit that I'd hacked into their system. Once done, Dr Weir pointed me in the right direction to grab some dinner.

I chose a table well away from the bulk of people and tried to eat as quickly as possible, hoping that nobody would notice me. I retired to my quarters to think about my day and try to soak away my aches from that mornings run. All too soon I'd have to get up and add some new aches but I was determined I'd never give Major Sheppard the satisfaction of seeing or hearing me complain.

Authors Note: I KNOW - stranger comes to Atlantis and just _happens_ to have the ATA gene - how convenient! And it's been done before ... many many many times! Apologies for the lack of originality BUT I had to give my character the gene otherwise she won't be able to do all the stuff that's coming up!

As usual, all the errors are mine and mine alone ... if you've been reading so far, thanks for your patience - I know the story is more centred on an original character that most ... mainly because my original premise for this story was that I'd really really like to go to Atlantis myself (what do you mean it's not real?!) - I decided to create Sabina Scott to go in my place.


	7. Let’s give it a few more weeks

**Chapter 7: Let's give it a few more weeks.**

It's hard to believe that I'd already been on Atlantis for over three months before I had the energy to contemplate my existence again. Major Sheppard had kept me busy the first week just with the morning runs and afternoon workouts. I'd then spent the rest of the day with one of Dr Weirs staff for training in the ancient and earth based technology which I luckily found a little easier to assimilate than all the physical stuff. Then I'd stumble to my room and sleep the sleep of the almost dead before doing the whole thing again the next day.

When Sheppard felt I was sufficiently fit enough to begin basic training my days changed. Mornings were basic training – after the first day of orientation these were lead by a grim faced marine named Sergeant Jones. I liked to call it basic torture – but only in my head of course. Major Sheppard sadly had _no_ sense of humour when it came to my training which I found out after the first day when he knocked me on my arse for wisecracking. Afternoons were Atlantis training and then some of the evenings were again basic training - the theory stuff also known as the _boring_ stuff which involved reading large volumes of material handed to me by Major Sheppard.

I did the physical training as well as weapons training including shooting practice – who knew it would be such a huge kick to shoot at things or that I'd actually be really really good at it – I think even Sergeant Jones was impressed although he never said anything. I also had to do first aid, survival and field training too.

I liked to put on a reluctant attitude each morning with Major Sheppard but really I was starting to enjoy the whole thing and I had never felt as good within myself. I even had a nickname – Scotty – yeah I know, not original, but Major Sheppard seemed to get delight out of calling me that and I had been thinking this was like Star Trek so it did seem to fit nicely. I of course only got to call him Sir .

There were a few days in between where I had to do the morning run by myself – Major Sheppard would just tell me he'd been off world on a mission (how cool does that sound!). Once though I knew he'd been hurt because I had to see Dr Beckett about something and saw him asleep in one of the infirmary beds. It really bothered me to see him looking so vulnerable like that and even Dr Beckett telling me the Major had been bitten by a particularly nasty bug but was recovering well didn't alleviate my concerns. I didn't visit him but I did ask Dr Beckett if he would pass on my regards – I don't know why he was so amused that I'd want to check on the Major! Only when Major Sheppard returned to our morning runs still able to kick my arse did I relax in the knowledge that he really was all right.

No one mentioned the ancient gene to me again which began to nag at me. I wanted to know more but Dr Beckett told me it was too soon. I was still in training and hadn't been assigned a permanent place on Atlantis. As for all those other tests – yeah you guessed it – didn't get to find out about the results of them either. I did assume that I wasn't nuts though because surely if the personality tests had shown that they wouldn't have let me run around the base and look at their computers.

Somehow Major Sheppard had forgotten I still had that laptop so I never gave it back. It had some basic information but the only new thing I learnt was that Dr Beckett had found a way to deliver the gene to those who didn't have it naturally. Someone called Dr McKay had this done first around the same time as that black shadow entity had been creeping through Atlantis. It worked on Dr McKay but in general only 49.8 percent of such treatments proved successful.

After all our morning runs I felt I'd gotten to Major Sheppard a little bit, finding him to be a lot more laid back than I had first supposed. This was a two edged sword because of course I wasn't as intimidated by his whole military tough guy routine anymore but as a result I was back to being much too aware of how attractive he was. Still I didn't feel up to confronting him about the gene either and ended up just going through the motions of each day getting more and more frustrated.

Thank god for the power of eavesdropping. Not that I set out to deliberately spy on anyone but if you heard your name mentioned before you entered a room wouldn't you pause for just a bit to see what was being said?

"When are you going to tell Sabina?" I overheard Dr Beckett's voice asking.

"Not yet," Dr Weir replied. "She still has a lot to assimilate before we throw something like that at her."

"She's gonna start asking questions Elizabeth," this was Major Sheppard's voice.

"She may work it out for herself," Dr Beckett added. "I've never seen the ATA gene so strong in anyone, even Major Sheppard. It's quite possible she can do things in this city that no one else can – she could stumble across something dangerous because she hasn't been told. She will need to do some practice to learn some control before we can just let her roam around the city more freely."

"Let's give it a few more weeks," Dr Weir urged. "Between the Majors training program and mine there's been little time for her to go off exploring. She's unsure of her position here – once she completes our training I'm sure she'll be receptive to helping us research the ancient technologies."

Was she kidding? Of course I wanted to explore Atlantis and try out any technology they'd let me get my hands on. I couldn't really see what the problem was and was all set to storm in there demanding to get started when I heard Dr Beckett's last comment.

"What about the other genes I couldn't identify?" he asked.

"Until you know what they do I see no point in worrying Sabina," Dr Weir replied. "Keep running your tests and let me know when you learn anything new."

Other genes? What the hell did that mean? Even though I had a meeting with Dr Beckett I found myself walking back to my room instead. Was I some kind of mutant human? Once again that horrible wash of panic and fear crept over me except this time it was more "there is something wrong with me am I going to die?" than "there are scary aliens who want to eat me". Suddenly I wasn't so keen to start exploring the city because the more I explored Atlantis the more I was sure I'd be exploring myself and that I wouldn't like what I found.

I decided not to say anything about what I'd heard. The only thing I could do was continue as I had been, hoping that Dr Beckett wouldn't discover something I really didn't want to hear.


	8. Now who’s getting personal?

**Chapter 8: Now who's getting personal?**

The next morning I met Major Sheppard for our usual run in the same pensive mood from yesterday.

"You know Scotty, basic training usually only lasts for 3 months." Major Sheppard spoke to me as we jogged down a deserted corridor. "If I decide to stick to that you only have a couple of days to go."

"That's nice Sir," I said, hardly even registering what he was saying. Yeah – I could even talk and run at the same time now and keep up with Major Sheppard although I suspect he was still taking it a bit easy on me.

"That's _nice_?" Major Sheppard asked, almost stopping to get a good look at me.

I of course didn't notice because my mind was fully engaged with worrying about how mutant I actually might be. I don't think I'd have even noticed that he wasn't running with me anymore if he hadn't caught up with me so he could grab my arm and pull me to a stop.

"Is something wrong Sir?" I asked, trying to pull my arm away but finding out that even though I'd been lifting weights he was clearly still a lot stronger than me.

"Is something _wrong_?" he queried in surprise. "I think the more pertinent question is, is something wrong with you? You've been quiet and distracted since we started running and that's not like you."

"You just said it yourself Sir," I evaded the question. "You've known me less than 3 months so you really don't know what's me and what's not. Maybe it's just that time of the month."

"Hey, no need to get all personal!" Sheppard let me go with a faintly disturbed look on his face.

I know it was cruel but seriously all men are the same – any mention of "women's" anything and they'd run for the hills. I didn't point out that if he'd known me 3 months then clearly he'd already experienced me during more than one of those "times of the month" and he didn't seem to work it out for himself. We continued our run without incident and parted ways. I fully expected him to have forgotten the whole thing by the next morning when I'd be seeing him again.

Usually I had all my meals in the commissary either by myself or sitting with some of the junior staff who were also doing some of the military training (not the early morning runs though – for some reason Sheppard reserved that particular torture just for me.) I hadn't been introduced to many of the senior staff apart from Dr Weir, Dr Beckett and of course the Major so if none of the junior staff were around I'd just sit in the darkest corner I could find and eat very quickly. That's what I intended to do that night so imagine my surprise when I'd just settled myself in a nice quiet corner only to be interrupted.

"Anyone sitting here?" that same cheery voice I'd begun to both dread and enjoy spoke loudly.

I looked up to see the Major with that smug smile he has, before looking down again with a mumbled "No Sir."

"Good, then you won't mind if I join you." Sheppard sat down and began to eat his dinner while completely ignoring the fact that I didn't want to chat.

"So you know, I was thinking about what you said this morning and I realised that I do know you well enough to know it's not that time of the month – didn't that happen like two weeks ago?"

"Geeze, now who's getting personal?" I asked in a harsh whisper, forgetting to Sir him as I looked around to see who might have overheard.

"I could continue asking you these very personal questions in a very loud voice," Sheppard threatened, "or you could just tell me what's bothering you and then I'll leave you alone."

"Fine ... Sir," I grumbled. "I was just worrying about the whole ATA gene thing," I semi lied because there was no way I was admitting that I'd eavesdropped.

"Sure you were," Sheppard nodded, looking at me intently. I tried to maintain eye contact but seriously than man has the most compelling eyes and I was beginning to think he could actually read my mind so I had to look away.

"Nice try," he approved, still smiling. "How about we give that another shot? And remember what I said about trust being an essential characteristic for Atlantis team members." Suddenly his face had that serious all business look. I knew he couldn't throw me out of Atlantis but he could see to it that I never got to do any of the really interesting exploration stuff that he knew I really wanted to do.

"I overheard you talking with Dr Beckett yesterday Sir," I rushed the words out really fast and quickly looked back down at my mostly uneaten dinner.

"And which bit has you the most worried?" he questioned in a tone that made me think somehow he was amused by me. Did he think this was _funny_?

"Oh I don't know _Sir_," I began in my starting to get annoyed voice, looking up again. "How about the fact that I'm in danger of setting off some ancient gizmo without meaning to because apparently I have too many ATA genes? Or the fact that I'm some kind of mutant human with DNA even Dr Beckett can't figure out? Or the fact that for some reason you all saw fit to keep it from me meaning it can't be a good thing?!" By the time I got to the end of that sentence I was almost shouting and my heart was beating so fast I'm sure he could see the beats if he just looked in the right place.

"Calm down," he grabbed my hands as I twisted them together in agitation. "First, there's no such thing as _too many_ ATA genes. Even I have to be careful touching new stuff because we don't know what any of it does."

"Okay, well what about the mutant gene thing and not telling me about it?" I quizzed him in a low fierce whisper.

"No one ever said those genes were mutant," he said in an exasperated manner. "Just because Dr Beckett doesn't know what they are doesn't mean they're bad. We just want to make sure we understand them because in this galaxy who knows what could happen. We could send you to some planet and find out those genes make you a rare and extra tasty dish for some neighbourhood Wraith!"

"Oh very reassuring Sir! Thanks for putting that mental picture in my head." I realised at that point that he was still holding my hands and it was getting me all worked up. I tugged on them but for some reason he didn't let go.

"Sa-bin-a," he elongated my name with some frustration. I felt a little thrill when he said my name because he hadn't called me Sabina since I'd started basic training. "You know you're being ridiculous don't you?"

"Stop calling me Sabina like that and stop holding my hands Sir," I commanded, still whispering of course. "People will talk!"

That only made him hold on tighter as he looked around the room to check out who was there. Most of his team were sitting at another table – he nodded at them and received some smiles in return before turning back to me.

"They already talk!" he said. "Even if there's nothing to talk about people just make stuff up. If you ever bothered to talk to anyone but me you'd know that!"

"Hey, I talk to people," I said starting to feel upset. Did he think I was antisocial or unfriendly? "I just don't gossip Sir! And since when was this conversation about my social habits instead of being about the fact that you were all lying to me?"

"We didn't lie to you," Sheppard said emphatically, dropping my hands to run his fingers through his hair in frustration. I knew this was something he did a lot which partly accounted for why his hair was always so messy.

"It doesn't matter Sir," I said jumping up quickly and grabbing my tray. "I have to go. I've got lots of studying to do and you know how Dr Weir gets if she thinks I haven't been doing enough."

"You can run Scotty, but it'll all catch up with you in the end" he said making it clear that he was letting me go ... for now.


	9. Call me John

**Chapter 9: Call me John.**

I fully expected that the next morning's run would be awkward but it wasn't. Major Sheppard greeted me as usual and we set off at a brisk pace. Do you know how absolutely cool it is to run a long way and hardly even break a sweat? It is totally cool! Even with everything I had on my mind, and believe me there was a lot including some things I hadn't even admitted to myself yet, somehow going for that run just put everything into perspective. I glanced across at the Major as we ran only to find him already looking at me. I raised an eyebrow in query and he smiled in return. "_Busted_" I thought. He knew how much I enjoyed all this and that my show of reluctance was just that – a show! I laughed and picked up the pace a bit, challenging him to keep up.

Usually at the end of the run we'd part company with just a wave and a "see you same time tomorrow" but not that morning. I was worried he was going to talk about the previous night but he didn't.

"So Scotty," he began. "Have you decided what you want to do to celebrate graduating from basic training?"

I looked up suddenly to find him grinning at me. "Graduating? You mean I've finished ... Sir?"

"Yes you've finished. Sergeant Jones tells me your skills are exemplary and you can almost outrun me. I'm really proud of you." Major Sheppard nudged my shoulder gently as we walked to cool down.

"Thank you Sir," I said quietly. Wow – I couldn't remember the last time I'd received praise like that.

"You know, now that you've graduated you're not under my command anymore and you don't have to call me Sir" Major Sheppard reminded me.

"But you're still the military leader," I protested.

"Key word there Scotty – military. So unless you were thinking of enlisting you don't fall under my jurisdiction except in matters of military security. I still expect you to train regularly and I hope you still want to join me for the daily run." Major Sheppard seemed to be almost hesitant when he said the last part which didn't gel for me because he was usually the epitome of confidence.

"Of course," I agreed quickly. "I'm still hoping to beat you one day!" I added as we continued down the corridor. I felt a bit numb actually – shouldn't I be more excited about this? I refused to acknowledge that a very tiny small deeply hidden part of me was just a little bit disappointed that I probably wouldn't be seeing as much of the Major any more.

"You don't seem as happy as I thought you'd be" Sheppard stopped walking to look at me more closely.

"I am of course but now I'm nervous too. Have you or Dr Weir worked out what my position is going to be?" I didn't add the Sir bit but at the same time I couldn't bring myself to call him anything else. I was so used to calling him sir or carefully calling him nothing at all.

"Call me John," he didn't ask so much as order – quite a contradiction since he'd just finished telling me I was no longer under his command. I noticed too that he'd completely ignored my question too.

"What am I going to be doing now ... Major?" I asked again, putting extra emphasis on his rank and making it sound like an insult.

"I'm not going to talk to you if you're gonna be like that!" he turned and started to walk away.

"Okay Okay JOHN!" I said it a bit louder than I'd intended making his name almost echo off the walls. I grabbed his hand and tried to pull him around to face me again. I'd forgotten about the jolt I always got when I touched him and flinched before quickly dropping his hand again. Since getting a similar jolt from Dr Beckett as well as from one of the scientists I'd met in the commissary a while back I'd decided my best bet was to avoid physical contact with anyone on Atlantis as much as possible.

He stopped and looked down at me in all seriousness. There was an intent look in his eyes I'd never seen there before and I began to feel that nervous rush like you get just before you know you have to get up in front of a group of people to speak. I tried to look away but found I couldn't. He gazed into my eyes for an eternity before seeming to find what he was looking for. Giving me a satisfied smile he put a friendly arm around me and steered me towards my quarters.

"You need to get changed and then we'll go see Elizabeth. She'll get it all sorted out and then you'll know where you stand. That'll be one less thing for you to worry about!"

"Hey – I don't worry about everything you know. Just the important things ... like what I'm going to be doing for the rest of my life!" I protested. In all honesty I _did_ worry about nearly everything but it bothered me he knew me well enough to know that.

"Sure, sure," he agreed while letting me know he knew I was completely lying. "After we get your day job sorted out you can think up some excuses for not going to dinner with me tonight."

"Dinner?" I squeaked. "Didn't we just do that last night?"

"Yeah but last night I was Sir and tonight I'll be John so it's a whole different thing. Like a date." I could see that John was trying not to laugh at the look on my face.

"A date? I'm not going on a date with you! I don't even like you!" I tried to protest but it was like trying to pin custard to a wall. Where did he get an ego like that and could I get even a small part of it for myself?

"Sure you like me – what's not to like?" Now he _was_ laughing at me.

"Laugh it up fuzzball," I almost growled that Star Wars classic. "There are things I like about you but they are far outweighed by the things I don't like about you!"

"You like things about me?" He was such a kid at times. Trust him to only focus on that part of what I'd said. "Go on, tell me more."

"Mmm, let me think," I mused. Maybe this was a chance to get my own back. "You're tall – that counts for something."

"Is that it?" he asked sounding almost disappointed. "That's just an accident of genetics, not something about me."

"Okay ... well I like the fact that you've got buns of steel. Gives me some motivation on all those runs!" I laughed now at the look on his face. Seriously he didn't know whether to be pleased or insulted by that one.

"Also not really about me – I didn't know you were this shallow."

Now that hurt a little. I forgot that I'd been trying to knock a few inches off his mammoth ego and took the whole thing to a serious level. "I like the fact that you always see the good in people first ...even though they might let you down from time to time. Doesn't really sit well with the Earth ideal of a military commander but somehow that's a strength in the Pegasus galaxy."

I looked down so I wouldn't have to see how he had reacted to that one and so jumped a little when I felt his hand under my chin lifting my eyes back to his.

"Thank you," he said with dignity. He still held my face up towards his and I seriously felt like he was 'leaning'. Was he going to kiss me? Crap, crap, crap! I was so not ready for that. Ducking under his arm I quickly walked the last few steps to my room, making sure the door was open before I turned back to him.

"See you tomorrow morning ... John." I tried to finish off our morning conversation on a predictable note.

"I'll pick you up at 19:00 hours," he replied. And then he just turned and walked off before I could protest.

"I'M NOT GOING ON A DATE WITH YOU!" I yelled at his retreating back.

"Sure sure," his voice carried back to me.

Authors note: I know it's a bit fluffy and there's more fluff to come ... but I do have my reasons, promise!


	10. How about this one?

**Chapter 10: How about this one?**

After I'd cleaned myself up for the day I was at a bit of a loss. John had mentioned going to see Dr Weir (I was a little ... disturbed at how easily Major Sheppard had become John ... at least in my head) so I decided I'd just do that by myself.

I paused outside her office just watching her tapping away at her computer. She was actually a pretty small woman but you didn't notice that because Dr Weir has an almost visible air of command about her. I was almost going to turn around and find somewhere to hide rather than interrupt her when she looked up and saw me standing there.

"Sabina," she greeted me. "Was there something you wanted?"

"Hi Dr Weir," I replied. "J – Major Sheppard graduated me from basic training this morning and I was just wondering ... have you worked out where you're going to place me yet?" I didn't meet her eyes both because I didn't want to see if she'd noticed I'd almost called Major Sheppard by his given name, and because I assumed she didn't know I'd overheard her in the infirmary the day before.

"Did he?" Dr Weir asked. "That's a few days earlier than I was expecting. Well done."

"Thank you," I acknowledged the praise with a small smile.

"I haven't had time to work out where we'll place you on a more permanent basis but for now I think Dr McKay could use your help with working out some of the ancient technology. Not many people have the ATA gene naturally and it seems that some of the rooms here just work better for people who've always had the gene. Would you be willing to help with that?"

"I'd love to," I agreed enthusiastically.

"Okay then, I'll introduce you to Dr McKay and he'll get you started. I'd still like you to continue with the training program I've been setting out for you. And if you're interested I'd like you to start learning to translate the ancient writing. We don't have enough people here who can do that – it might help with working out what some of the labs were for."

I felt a leap of nervous excitement at the idea of learning to translate ancient. Dr Weir had said not many people could do that and I admitted to myself that this was a large part of my interest in doing it. At the back of my mind I was always aware that I had stolen a spot here at Atlantis – not that I'd pushed anybody else out but I wouldn't be here if I hadn't been swept along in that group of people who DID belong here. If I learnt something that was really useful that most of those people didn't know then maybe I'd begin to feel more like I belonged here too.

"Thanks Dr Weir," I said gratefully. "I know I shouldn't ... that is I know it must be hard to find somewhere for me to fit in and I really appreciate the opportunities you've given me."

"Not at all Sabina," Dr Weir denied. "It's great to have someone with the ATA gene to help Dr McKay. Major Sheppard is usually his first choice but the Major can't often spare the time Dr McKay needs. You're helping more than I can tell you – Dr McKay can be ... difficult ... at times when he feels the same priorities aren't being placed on the projects he personally feels are the most important."

With that we headed down to Dr McKay's main lab where I was introduced to the man I'd heard was the smartest person on Atlantis for the first time.

"Yes yes," Dr McKay hardly acknowledged my presence when Dr Weir introduced us before departing for a meeting. "Welcome and don't touch anything you don't understand by which I mean don't touch anything ... at all"

"Okay," I replied. "but I thought the reason I was here _was_ to touch things you hadn't worked out yet ..."

"I know what most of the things we've found do," Dr McKay protested, looking at me for the first time. His blue eyes shone with sharp intelligence and I fully believed that he really was the smartest person here. "I just need someone with the gene to power things up so I can take readings, map power levels, that kind of thing."

"That I can do," I agreed with a smile. "And if it means you get to progress things without having to rely on Major Sheppard making time for you then I like that even better."

"Already acquainted with Major Sheppard's views on our priorities are you?" Dr McKay suddenly seemed a lot friendlier. "Shoot first and do the science research after – and if you can't understand what it does then just blow it up!"

I laughed, and almost at once relaxed the muscles I didn't know I'd been holding so tensely. I could tell I was going to like Dr McKay. I know his manner of always speaking exactly what he thought, and in a condescending way at that, would offend a lot of people. Not me though – I had always been a "what you see is what you get" kind of girl and I fully respected someone who would tell it to you like it was and not pull their punches.

"So when do we get started?" I asked.

Dr McKay wanted to get an idea for how proficient I'd be with the ancient technology first so he took me to another lab and showed me an array of gadgets he'd been trying to work out.

"These are some of the things we've found in our explorations," he said. "So far only Major Sheppard has been able to get any of them to work easily – unfortunately they seem to be the type of Ancient technology that requires the user to have the ATA gene."

"Okay," I said a bit nervously. "What do I do?"

"Just pick something and we'll see what happens when you touch it," Dr McKay instructed me, already bending over his data pad.

"Right," I said, looking more closely at the gadgets I had to choose from. One seemed to draw my attention more than the others – it was large and round in shape, with a series of ancient markings carved around its edges.

"How about this one?" I indicated my choice.

"That will do fine," Dr McKay said a bit impatiently. "Put your hand on it."

I placed one hand carefully on top of the device in the middle of the circle. Blue lights immediately lit up inside it and the nearest display screen began churning out lines and lines of characters I could only assume were the Ancient language.

"What is all that?" I asked curiously.

Dr McKay motioned impatiently for me to stop talking as his eyes moved rapidly over the display.

"It's some kind of weapons research inventory I think," he muttered. "Most of it is incomprehensible but I recognise some of it as being statistics on some tests they were doing with the command chair. I'll need to download this to my machine to analyse it further," he added, beginning to walk out of the room.

"Uh Dr McKay?" I called out to him. "Are we done here?"

"Oh," Dr McKay looked back at me with that puzzled look I was to learn he often got on his face, the one that said the next step should be obvious and why was he surrounded by people too stupid to work that out for themselves.

"I'll be back with my laptop in a minute," he said distractedly. "Just wait here." And then he just left me there, muttering to himself as he continued down the corridor.

I closed my eyes and enjoyed that first feeling of having accomplished something in Atlantis. As I did so I couldn't help but think how badly I really needed to know more about the ancient gene and whether those extra unknown genes were connected in any way. I opened my eyes again and noticed that one of the other gadgets had lit up. It was a small data pad, again displaying lines and lines of Ancient text – they seemed to be calling out to me and even though I knew I'd probably get in trouble later I reached out and grabbed the device. I didn't want anyone else to read what was on there because I assumed it would be something about my mutant genes so I consciously tried to think "off". The device became dormant again and I quickly shoved it in my jacket pocket just as Dr McKay returned to the lab.

Feeling a bit breathless, I helped Dr McKay get all the information he could from the circular device. The whole time I was so aware of the data pad in my pocket it surprised me that Dr McKay noticed nothing. I was relieved when he told me he had enough for now but not to go too far in case he needed me again.


	11. This is not a date!

**Chapter 11: This is not a date - it's just two people meeting to consume their necessary daily nutritional requirements.**

Dr McKay had cut me loose earlier than I'd expected which allowed me to head back to my room without having to make up excuses. The palm pad (that's what I'd decided to call it because it was a data pad that fit into my palm) was burning a hole in my pocket and I desperately wanted to check it out further.

Once locked in the privacy of my room though I found only more disappointment. The palm pad powered up again as soon as I held it in my hand but no matter how much focus I put into thinking that I really needed the symbols translated into English nothing happened.

Dr Weir had already offered to get me learning ancient and now I had even more motivation to make that happen as soon as possible. I was so frustrated because although the ancient language just looked like a lot of boxes and lines rather than writing I felt that if I just looked at them for long enough I'd be able to understand what they said.

Realising that staring at the palm pad was only giving me a headache I resolved to accept that it would be some time before I'd be able to access the information it contained. Now I just needed to find a hiding place. As usual, as soon as I thought about something I really needed my room provided the solution. Even though this wasn't my original room the same principle still seemed to apply. A panel on the wall started blinking those same blue lights at me that all ancient technology seemed to emit. I walked over to discover some kind of wall safe. Placing the palm pad inside I stepped back and watched as the panel returned to looking like every other panel on the wall. Worried that I wouldn't be able to get it out again I waved my hand over the panel and was relieved to see the safe reopen.

Okay, so there was another problem I had been forced to put on the back burner. I still had most of the day free so I went back to Dr Weir to get my first "let's learn to read Ancient" lessons. She set me up with my very own laptop (making me feel even guiltier about the one I'd borrowed and not returned) with the lessons already loaded. Apparently someone called Dr Daniel Jackson back on Earth had set up the programs to try to encourage more researchers to learn to translate themselves rather than rely solely on him.

Rather than return to my room I decided I'd find a nice, out of the way spot to begin. Not because I was avoiding anyone (honestly) but because I really didn't want to have witnesses to my first clumsy attempts at even understanding the basic constructs of the ancient language and because I knew if I stayed in my room the very presence of that palm pad would drive me to distraction. As far as I knew, no one even knew where my old hiding room had been and I decided the balcony would be an ideal place to study.

The hours dissolved without my notice and the only thing that reminded me of how late it had gotten was my stomach letting me know it had been too long since I'd last put anything in there. I hadn't forgotten Major Sheppard's threat to pick me up at 19:00 hours but it wasn't actively at the forefront of my mind. I headed back to the commissary and grabbed my usual tray of dinner items before finding a dark and quiet corner to eat in.

The Ancient language was so fascinating, particularly the links between it and our Latin. I was already obsessed with learning as much as I could as rapidly as I could - I'd set up my laptop so I could read and eat at the same time.

And that's how Major Sheppard found me just a few minutes later.

"Sabina," he greeted me. "I'm kinda hurt that you didn't wait for me."

"Huh?" I looked up having not registered his actual words and was surprised that I hadn't noticed his approach. "Major Sheppard," I greeted him. "Did you want something?"

"Oh I want a lot of things Scotty but now's not the time to get into that," he replied with a sly grin. "For now I'll just settle for that dinner date we planned this morning."

"You mean that date _you_ planned that I never agreed to?" I asked in exasperation, deciding to ignore the nervous feelings the first part of his response had provoked.

"That would be the one." Clearly he was not moved at all by my reluctance. "Move over so I can sit down would you?"

I could see that he wasn't going to be swayed on the whole eating together thing so I reluctantly closed off my laptop program and shifted to make room for him.

Looking up at him I couldn't help but add "But this is not a date - it's just two people meeting to consume their necessary daily nutritional requirements."

"Sure sure," he replied, sitting down and taking up way too much room.

Have you ever noticed how some men do that – take up all the space in a room no matter how big it is? It's not even solely a physical thing – with John it was as much his command presence as it was his physical size that seemed to absorb all the air around us, making me feel both crowded and short of breathe.

"So," he said after a few minutes of silence. "How was your day dear?"

"Funny," I said with a straight face. "Actually it was pretty good. I got one of those ancient devices to power up – Dr McKay was really excited because it was something about weapons research!" I couldn't help but brag about my small victory.

"Really? Cool! Now Rodney can pick on you to be the guinea pig for all his "what does this ancient doohickie do?" experiments." Major Sheppard didn't seem at all bothered that his reign as the most proficient ATA gene carrier might be over – not that I thought I was as good as him by any stretch after just one morning of good luck.

"I really don't mind," I said. "I'm looking forward to working with Dr McKay."

'Wait a minute," John protested. "You actually liked Rodney? The same Rodney who thinks that everyone is his intellectual inferior and makes sure we all know it?"

"I _am_ his intellectual inferior," I reminded him. "Why would I take offense that we both know it? Besides, it's kind of refreshing to be around someone knowing where you stand and what they really think of you. I could do with a little more of that in my life."

"Listen," he had a hold of my hands now and was using them to pull me closer to him. "One – you are not intellectually inferior just because someone else happens to know more about a subject than you do!"

I could hear the frustrated tone in his voice but I really wasn't interested in having my ego artificially propped up. I tried to pull away but he held on.

"I'm not done yet," he said. "Two – it's not always a good thing to know exactly what everyone else is thinking about you. You might not be ready for that big a dose of honesty."

"Maybe," I agreed because we both knew I was so not ready for any level of honesty about _his_ opinion of me. "But I still think things are being kept from me deliberately and I really hate that feeling!"

"I can understand that," he replied. "So long as you _try_ to understand that we're not keeping things from you that have any bearing on what you're trying to establish here."

"So you _are_ keeping something from me?" I jumped on that one part of his statement.

"NO," he squeezed my hands to emphasise his point. "There are some things to do with the security of this base and this mission that you cannot be privy to but that makes you no different from 90 percent of the members of this expedition."

"Oh," I said in a small voice, looking down as I realised that I'd been making my situation more important that it could possibly be to the leaders of this expedition.

"Now don't go all timid on me," John protested. "I will try to keep you informed whenever I can but there will be some things I won't tell you for your own safety. Wouldn't want the Wraith getting hold of you and sucking compromising information out of you just because you're in with the boss now would we?"

"Geeze, would you _stop_ putting nightmare inducing Wraith scenarios in my head!" I pulled away from him and stood up to leave the table. "And I'm not 'in' with the boss ... don't treat me any different that you would any other person you've trained!"

"See now that's a problem," he drawled as he got up and followed my hurried dash from the commissary. "Like it or not, you _are_ different from all the other people I've trained."

"No I'm not," I disagreed. "And _stop_ following me!"

"My grandmother always told me I should escort a lady to her door after a date," he said, using his longer legs to easily match my strides as I turned down the corridor towards my room.

"THIS IS NOT A DATE!" I yelled the words, turning and using my hands against his chest to push him away. In my annoyance I had clearly forgotten that he was _much_ stronger than me and that trying to push him away would be no more successful than trying to move a mountain.

"There's no need to yell," he grabbed my hands and held them against his chest, clearly not at all bothered by my protests. We'd arrived at my room and even though I had believed that only I could activate the controls John proved this to be incorrect when he swiped open the door and backed me inside.

Can I just say at this point that I was seriously worked up and not thinking clearly? Some tide of emotion had me in its grip and I really don't think I can be held accountable for my actions.

"What are you doing?" I asked a bit breathlessly.

"Well if you have to ask then I'm obviously not doing this right," John replied in a predatory, quiet voice right before he backed me against the adjacent wall and kissed me.

Authors Note: Apologies to anyone cringing at the fluff stuff - I liked this story a lot better when I was writing it than I do now I'm posting it! I'll keep going though ...


	12. It’s not just lust you know

Authors note: Warning ... this chapter contains some sexual references

**Chapter 12: It's not just lust you know.**

That panicked and yet excited wash of emotion I'd started to become too familiar with stormed over me immediately, along with a heady rush of adrenalin. It wasn't your average "Hello - nice to kiss you for the first time" kind of kiss either. John drew me in like he'd been kissing me forever. He was fire and passion – lips melding to mine, tongue instantly blazing through my defences to claim every inch of my mouth, body rocking against me in all the right places as his hands began to explore. I was kissing him back just as feverishly and straining to get closer before I knew what was happening.

I can't speak for him but I felt a connection to him like I'd never had with anyone else that contributed to how quickly those intense sexual emotions overtook me. I have no doubt that I would have participated to the obvious conclusion if he hadn't pulled away before we got quite that far.

My hands were buried in his hair and his were up my shirt and splayed across my bare back still holding me tightly to him. Breathing deeply John rested his forehead against mine as we both recovered from the storm of emotions.

"Okay, that was a little more intense than I was expecting," he said, trying to lighten the mood.

I was starting to come back to myself and the realisation of what I'd just willingly participated in. What had I been thinking!

"That was a mistake," I said, ignoring the fact that he'd obviously been thinking about kissing me before he'd actually done it. I attempted to pull away with the hope I could put some distance between me and his disturbing presence but he wouldn't let me.

"Oh no," he said. "We're not going back to the whole denial thing. I only stopped because I don't want to screw this up by going too fast. There's no way I'm gonna let you forget what we'd be doing right about now if I hadn't called a halt - with both of us fully participating!"

"So I'm not immune to the effects of lust," I tried to make light of my feelings. "But like I said – it would be a mistake for me to act on those feelings with someone in your position, Major."

"Don't put my rank up as a barrier between us," he said, finally letting me retreat to the other side of the room. "There're no rules or regulations governing any kind of relationship between us."

"So we just engage in a few bouts of mindless sex and then go our separate ways?" I asked in disbelief. "That might work for you but for someone like me it would spell disaster. Atlantis is a small place – it would get around before you'd made it all the way out my door and I'd be the one no one would ever take seriously again."

"Someone _like you_?" John was clearly getting angry with me now. "What's that supposed to mean?"

"Don't play dumb Major," I almost sneered. "We both know that I'm teetering on the lowest rung of the Atlantis ladder and that if we could have dialled Earth I'd have been shipped back before the dust had even settled."

"Sabina," he protested, anger suddenly gone. He tried to reach for me again but I was having none of that.

"Stay over there," I ordered him. "I can't think when you get up in my face like that."

"You think too much," John muttered under his breath, running his hands through his hair. God I loved his hair ... and his eyes ... and the way he towered over me ... and ... oh god what was I doing?

"Look, I'm not up to discussing this any further tonight." I stated firmly. "I've had a long day and my brain feels like it's about to explode with too much new stuff. Can we just drop it for now, please?"

"Sure, I can do that," he agreed. That had been almost too easy – what was he up to now?

"Same time tomorrow morning?" he asked casually as he headed for the door.

"Um ... okay" I said hesitantly, following him without even thinking about it.

Once in the corridor again he turned to face me. I had assumed that he wouldn't want anyone to see us together in a non platonic sense and it was still early so I felt safe in standing in the doorway to see him off.

"Goodnight Scotty," he said before pulling me to him and giving me a passionate farewell kiss. My brain went into overdrive. He didn't hold anything back and I was feverishly participating with no thought for who might be walking by.

Oh the humiliation of realising that once again it was John with the control enough to pull away leaving me wanting more ... and I seriously wanted a lot more at that point.

"It's not just lust you know," was his parting line before he turned and swaggered off down the corridor whistling a jaunty tune.

I floated in a daze back inside my room, troubled by what had happened. Even though on the surface it seemed John was interested in me I knew that when it really counted he was light years out of my reach.


	13. There is no we!

**Chapter 13: There is no we.**

When Sheppard (I'd decided that from now on I was only going to call him 'Sheppard' – just like his other friends did) greeted me the next morning for our daily run his manner was such that no one would have believed only a few hours prior he'd had his hands up the back of my shirt.

Maybe our run was a little more ... competitive ... than usual but for me that was more about trying to outrun the thoughts I really didn't want to be having about my companion than anything else. As we turned the last corner heading back to my room Sergeant Bates approached and told us Dr Weir wanted to see both of us straight away.

"I wonder what she wants," I worried, feeling a bit like a school kid being called to the principal's office.

Sheppard said nothing as we changed direction and headed for Dr Weirs office, and his silence only made me worry more.

"Sabina, John," Dr Weir greeted us in a friendly yet reserved tone.

"Elizabeth," John replied, raising an eyebrow to query the need for both of us to meet with her.

"This is awkward," Dr Weir admitted after a prolonged silence. "Dr Beckett came to see me this morning to warn me about the latest gossip making its way around the city. Do you want to guess what that might have been?"

My face reddened as I realised where she was going with this – someone had seen us last night. I kept my eyes away from Sheppard and firmly fixed on the floor, I'm sure giving the appearance of a naughty child.

"Since when has Atlantis gossip been of interest to you Elizabeth?" Major Sheppard's tone said he was both surprised and annoyed that this was what Dr Weir had wanted to talk about.

"Since it involved the _ranking_ military officer and someone supposedly under his command!" Dr Weir replied in a more heated tone. "What were you thinking John, or were you even thinking at all?"

"I didn't realise I had to clear how I use my personal time with you first!" John retorted. "Sabina has finished basic training and I made it quite clear that she is no longer under my command – what we do in our own time should be of no concern to anyone but us."

I'm sure my face got even redder at that point – he was making it sound like a lot more was going on than there actually was.

"There is no _'us'_," I protested weakly, glancing up to see both Dr Weir and Major Sheppard frowning at my interruption.

"You're right," Dr Weir directed that one at John, ignoring me completely. "I'm sure it will get around just as quickly that Sabina has finished her basic training but it would have been better if you'd waited until that was the case. You have every right to engage in a relationship with any of the civilians here BUT you have to be aware of the strain this might place on Sabina."

"People are going to think I'm being favoured because I'm," I glanced at Sheppard and queried "how did you put it 'in with the boss', aren't they?"

"Maybe initially, until they get to know you," Dr Weir admitted.

"This is all bullshit!" Major Sheppard protested.

"Major," Dr Weir cautioned. "I didn't call you here to reprimand you, just to warn you. I'm sure you don't want people gossiping about Sabina, and burying your head in the sand because it annoys you that they are isn't going to help either of you."

"Okay," Sheppard admitted. "We appreciate the heads up."

"THERE IS NO WE!" my shouted comment effectively silenced both the Major and Dr Weir. "Perhaps you could spread that piece of gossip around instead," I suggested in a quiet voice to Dr Weir before turning and making a hasty exit. I knew that was beyond rude and that I would have to apologise later but I seriously hated the idea that people's opinion of me would be dictated by something I hadn't even done. That fact that I really really _wanted_ to do what I was being accused of only made it worse.

I paused outside the door to try and get myself under control, and I couldn't help but stay there once I'd begun to overhear the rest of their conversation.

"Shouldn't you go and talk to her?" Dr Weir asked.

"Nah – she just needs a little time to realise that this isn't as big an issue as she thinks. I know what I'm doing," Sheppard reassured her.

"Do you John?" Dr Weir questioned. "Because I have to say I'm a little surprised at the way you're going about this. I never expected you to let personal situations get in the way of your command on this base."

"I _haven't_ let personal anything affect my command, Elizabeth," he protested heatedly. "I've known Sabina for 3 months – have you noticed in that time that I've put anything ahead of my military duty?"

"Of course not," Dr Weir admitted. "To be honest I didn't notice anything out of the ordinary between you and Sabina until Carson brought it to my attention this morning."

"_Thank you_," Sheppard almost overemphasised. "Look, I'm just as surprised as you that I even have any personal situations to deal with! But there's a connection there Elizabeth, something I felt the first day when I saw Sabina step through the gate before I even knew anything about her. And my gut is telling me it would be a mistake to ignore that connection – that somehow the good of this whole mission might rest on it."

I didn't even want to hear what Dr Weir might make of that – turning quickly I ran back to my room. Once there I almost collapsed on the floor, putting my head in my hands as I leant on my bent knees. He felt it too? Rather than relief that I wasn't the only one I felt scared. There was something about Atlantis, something about me ending up here that had always seriously worried me. And now knowing that Sheppard felt some of that too just worried me more.

What did it all mean? Rubbing tiredly at my forehead I frowned in concentration. It was all tied in with the ancient palm pad I was hiding – very glad I hadn't told anyone about that – I had to be able to understand what was on there and to do that I had to understand ancient. So really I was back where I'd started out this morning – learning ancient was still my top priority and I resolved to let nothing get in the way.

For the first time I tried to deliberately command my room to do something for me. "Let no one including Major John Sheppard in" I commanded. A few minutes later when I heard Major Sheppard outside my door I was relieved that this time he wasn't able to open the door without my permission. Putting everything else out of my mind I settled down with my laptop. It was time for some serious studying.


	14. How long are you going to do this?

**Chapter 14: How long are you going to do this?**

Luckily for me Sheppard had a lot of responsibilities on Atlantis and he did seem to take them all very seriously. A part of me had been expecting him to be waiting to ambush me when I left my room several hours later but thankfully that wasn't the case. Hopefully I'd be able to pick up some food and make it back to my room before anyone I didn't want to see could find me.

Once in the commissary though I realised there was at least one person I couldn't avoid. Dr Weir was sitting at a table by herself, obviously finishing her lunch. I made my way slowly over to her, trying to decide what I was going to say.

"Uh, Dr Weir?" I interrupted her lunch, standing nervously across from where she was sitting. "Have you got a minute?"

"Of course," Dr Weir replied in her usual professional way.

"I just wanted to apologise for my outburst this morning," I said quickly. "You were just trying to help and I shouldn't have taken my frustration out on you."

"That's quite all right Sabina," Dr Weir's smile was both friendly and forgiving. "I can appreciate how you must be feeling right now and to be honest I don't envy you having to deal with a determined Major Sheppard. He can be ... difficult ... to derail once he's decided what path he's going to take in a military situation and I'm not surprised he'd be similar in his personal life."

"Yes well," I began to feel uncomfortable with the personal turn the conversation had taken. "like I said there really isn't an 'us' and I'm sure before too long that will all be resolved. In the mean time I just wanted to reassure you that I'm fully committed to earning my place here and that I don't intend to let personal issues get in the way."

"No one expects you to work 24/7 Sabina and only the military have rules about fraternisation," Dr Weir said with an almost amused look. "I wouldn't underestimate John – it's been my experience so far that he's a lot smarter than you might expect and that he seems to always find a way to get what he wants while making you think it was your idea."

I made a non committal sound in response to that, thinking I should really leave before this got any more uncomfortable.

"If you ever need to talk to someone Sabina, about anything," Dr Weir's tone held a hesitant caring quality now. "I hope you know that my door is always open."

"Thank you," I said gratefully, determined that I'd never take her up on that. "I should let you get back to your lunch."

I decided that the only way to deal with the situation was to avoid Major Sheppard. I could have just sat down with him and explained all the reasons why I thought us spending personal time together was so not a good idea. But I knew what would happen - he'd listen to all my protests and nod like he completely agreed and understood my position and then before I knew what was happening I'd be waking up in his quarters instead of mine.

The first chance I got I had asked Dr McKay why is was such a big deal that I'd remained hidden on Atlantis for a few days and he told me about the life sign detectors and city wide sensor system. I should have shown up on those when they were looking for Jinto during the day that he was missing after letting that ... shadow entity ... out of its cage. The sensors couldn't pick out a particular person but a lone signal in an unoccupied part of the city would have given me away. Dr McKay said in thinking about how much I wanted to stay hidden I must have accessed the sensor system and made myself "invisible" - told the system to ignore my specific life sign. Pretty cool huh?

Over the course of that day with a bit of reshuffling I made my daily schedule pretty much Sheppard proof. Mornings I'd organised to train with Teyla, who seemed happy to accept my explanation that I wanted to learn the fighting sticks with her. When she was not off world we would warm up with a run before she conducted my training session. She had tried to talk to me about Major Sheppard before agreeing to train me but I think my genuine desire to learn defensive techniques as well as anything else I could to make myself a useful member of Atlantis convinced her that my motives were not just about avoiding the Major. I don't know why but Sheppard never tried to interrupt these sessions so I could only assume that Teyla spoke to him about it.

Once I'd completed my session with Teyla I'd head straight to the mess to get breakfast with all the other junior members - I'd worked out a group of them met the same time every day and I just insinuated myself with them. I'd seen Major Sheppard come in a couple of times and look for me - I guess Dr Weir's warning about how people would talk was enough to hold him back from just coming over and yanking me away. The first day I did this, the day after my meeting with Dr Weir, I was put on the spot when one of the junior scientists asked me outright what the deal was with me and Sheppard. I laughed and said it had all been a misunderstanding and that now I was no longer in basic training I hardly even saw him anymore. I guess that was convincing enough because no one asked me about him again after that. Luckily they didn't seem to mind my presence so I was able to join them for the evening meal too.

I'd spend the mornings with Dr McKay or Dr Zelenka if McKay was off world, doing all those guinea pig tests Sheppard had complained about. Afternoons I'd hide out in my old room learning ancient and continuing the other lessons Dr Weir had set for me. I'd asked Dr Zelenka for some other learning materials to do with the ancient technology and he happily overloaded me with gigabytes of information to read. Having the ATA gene helped because I'd just make the sensors not register my presence at all - in fact I did that pretty much all day. At first the mental effort of maintaining that sensor blind spot was so great that I found it hard to concentrate on anything else. Over a few days I learned how to keep the block at the back of my mind so I could concentrate on other things. In the end it was just like breathing – I didn't have to consciously make an effort to do it, it became part of my brains usual activities. I also made sure that Major Sheppard couldn't override the lock on my room like he had that one disastrous time - even with a sensor blind spot he would know I was there every night.

It helped that there was a crisis in Atlantis at the same time that I began to avoid Major Sheppard. Teyla told me that in five of their last nine off world missions they had been ambushed by the Wraith. That couldn't be coincidence ... horrible as it seemed, the only thing that made sense was that there was a Wraith spy in Atlantis. I was glad there was no way I could be suspected – being a stowaway and all.

I could tell Teyla was troubled one morning – when pressed she admitted it saddened her that the Athosians had left Atlantis to settle on the mainland ... more so when it was discovered that there was no spy at all, just a hidden necklace transmitting their position to the nearest Wraith ship. Major Sheppard decided to use that fact against the Wraith, managing to capture one and bring it back to Atlantis for questioning – a fact that frankly freaked me out.

Crisis aside, my avoidance plan was going really well which bothered me a little - didn't Sheppard want to talk to me? He didn't seem to be making much effort to find me - not that I wanted him to but still it would have been nice to be able to more actively show him that I was avoiding him! I was in Dr McKay's lab one morning a few days after the Wraith spy thing was resolved when all that changed.

"Rodney," I heard Sheppard's voice from the doorway and tried to hunch myself down low so he wouldn't notice me. "I need to borrow Sabina for a moment." Okay so obviously he already knew I was there.

"No no no," Dr McKay protested. "I finally have someone who's willing to help me - I might have the ATA gene myself but I can't concentrate on operating things and take all the readings I need at the same time. Sabina's a natural ... in fact she's better than you in some respects." Dr McKay looked slyly at Major Sheppard at that point to see if his little barb had hit home. He should have known that Major Sheppard just didn't care about that sort of thing.

"I only need her for a minute McKay," Sheppard drawled, not looking at me. "You can have your guinea pig back after that."

"Oh, all right. Just don't upset her because her control gets a little wobbly when she's upset." Dr McKay turned back to his laptop without even glancing my way. He really was in his own little world and completely oblivious to the undercurrents between the Major and me.

"Hey," I protested more heatedly than the situation really demanded. "Don't I get a say in this? I don't think we should interrupt this experiment - I just got the right ... _hey_!" I protested again as Major Sheppard grabbed my arm and dragged me out of the room after him.

Still not saying anything to me he swiped his hand over a door panel just down from Dr McKay's lab and I found myself in a storage room crowded with boxes. Sheppard released my arm as soon as the doors closed behind us and took a step back so we were as separated as we could be in such a small space. He stood there just looking at me but I was determined he would speak first.

"It's been _two_ weeks,' he finally said. "How long are you gonna do this?" he asked without any hint of the anger I was sure he must be feeling by now.

"Do what?" I asked innocently, before relenting when I saw the knowing look on his face. "Okay okay," I admitted. "I didn't want to talk about ... anything ... with you right now and I didn't think you'd feel the same way so I just thought a little space would be a good idea."

"I'm not gonna jump you every time I see you," he was teasing me now. "I do know how to control myself ... pretty sure I already demonstrated _that_ when I ..."

"Don't!" I interrupted before he could finish. "Don't you _dare_ bring that up now - you pulled back first but we'll never know whether I would have pulled away myself if things had gone any further!"

"Oh I'm pretty sure we both know exactly how that would have ended if I hadn't stopped us," he was getting a little riled up, "an action I'm regretting now I know how good you are at the whole avoidance thing!"

"You may be the Poster boy of Atlantis but that doesn't mean every woman wants you mauling her," I hotly tried to redirect the conversation.

"Mauled? _Poster_ boy?" Sheppard suddenly looked a lot more than riled and I realised that challenging him had probably not been the smart thing to do.

I put my hand out at chest level when I saw he was about to step closer. "You stay over there," I directed weakly.

Instead of replying Sheppard just grabbed my outstretched hand and used it to pull me roughly the rest of the way to him. All the breath rushed out of me as our chests collided and before I could take another one I was overwhelmed by the kiss of an angry Major Sheppard. This one was different from those first kisses - he still kissed me like he had every right to but this was a little rougher and a lot less controlled.

I'd like to say that I held firm to my resolve and didn't participate but we all know that's not what happened. It only took moments for me to lose it - that jolt of energy I always got from him was so strong this time, forcing me to cling to him in order to remain standing. The next few minutes were all about mouths engaged in battle ably assisted by hands roaming where they really shouldn't have been during working hours. I was completely lost to myself and I think this time so was John. We really would have consummated our relationship on top of a box of notepads and spare laptop batteries if the sound of his radio beeping hadn't pulled us back to reality.

I pulled away almost guiltily, rebuttoning my shirt (when had he opened that?!) and smoothing my hair back into its usual pony tail. I then slumped onto one of the boxes and put my hands over my face, wondering how many times that radio had beeped before it registered.

Major Sheppard was talking into his radio but I only registered the last bit of his conversation. "Yes I'm sure I'm okay! I'll be right there Teyla," he confirmed before turning the radio off and looking back to me.

"There's a problem on the mainland and Teyla needs me to fly her over," he said. I resented the fact that he appeared unaffected by what we'd just been doing while I felt that standing up right now would be more than I could manage.

"Look, I ..." he began, running his hands through his hair - maybe he wasn't as unaffected as I thought.

"You don't have to say anything," I stopped him. "You go help Teyla and I'll just go back to avoiding you."

"You do that,' he said with a laugh. "I'll ambush you again later," he added before turning and walking out the room.

Rather than wait for Sheppard to find me I decided to go on the offensive instead. I didn't want anything too private so when I saw him sitting in the commissary by himself the next morning I joined him.

"Can we talk?" I asked quietly, sitting across from him.

"Not avoiding me today? Major Sheppard teased.

"Wasn't really working, was it?" I admitted. "Look ..." I paused, trying to organise my thoughts into some kind of logical order. "I'm not ready for this ... whatever this is between us. I'm still finding my way here and I can't concentrate on what I need to do when my focus is so divided."

"I'm not trying to makes things difficult for you," the Major protested.

"I know, I know," I let him off the hook. "It's me. I just need some time to get used to everything because frankly the fact that I'm even on another planet still freaks me out."

"I can give you time," Major Sheppard agreed easily, "so long as we're clear that you're not gonna go messing with anyone else in the mean time."

"I think that's a pretty safe bet," I laughed, thinking it was doubtful there was anyone else on Atlantis crazy enough to want to get involved with me. "Friends?" I asked hesitantly, holding out a hand to shake on the deal.

"Friends," he agreed, grasping my hand and squeezing it firmly.

"Good," I said with relief. "I'm glad that's sorted."

"Helping McKay again today?" Major Sheppard queried, thankfully changing the subject at last.

"Yeah – he's still excited about that weapons thing – even though we haven't been able to get much more than that inventory from the first day. The Ancients weren't very good at leaving instructions, were they?

"Not so much," he agreed as he rose and gathered up his rubbish. "I've got a mission so I'll catch up with you later." I smiled as he sauntered away, stopping at the entrance to throw me a half wave. It was a relief to be on better footing with the Major again.

The next month passed very quickly. I got to know Major Sheppard much better and found that, overwhelming attraction aside, he was an entertaining and interesting companion. The bonus was that I got to know Teyla, Dr McKay and Lt Ford much better as well and could see why the Major had begun to consider them his surrogate family. Although Sheppard made no further physical advances, he flirted with me at the least opportunity, often making me blush with his innuendos. Sometimes he'd ask me out on a date but I always managed to find a way to change the subject without offending him. I found it difficult at times to resist his boyish charm and good looks but I was unwilling to risk our budding friendship for something I was sure wouldn't work out in the end.

Sometimes I would get to sit with Major Sheppard and his team after they'd returned from an off world mission and hear about what happened – details I wouldn't have heard otherwise. To be honest, those missions all seemed a bit sad to me, in different ways.

I couldn't decide whether the mission to M7G-677 was good or bad. It horrified me that there was a planet of children who believed that the Wraith would stay away as long as they killed themselves before they turned 24. I was sad for all the 24 year olds who never made it to 25 but at the same time happy that Major Sheppard had managed to convince their current leader Keras not to follow that blind tradition.

The situation on Hoff was especially troubling to me. Here was a race so desperate to defeat the Wraith they were willing to sacrifice half their people to make it happen. Would there come a time when _we_ would feel that desperate? The fact that we had been willing to give them our Wraith prisoner when we knew they would be experimenting on him seemed to suggest that maybe we would – although I found it hard to ignore the sense of relief I felt in knowing that the Wraith was no longer on Atlantis.

The worse mission of all during that month was the one to the Genii home world. I could see that this one troubled Major Sheppard on a number of levels. The fact that a potentially strong ally would rather use us and betray us instead of joining our fight against the Wraith angered him. Going to that Wraith hive ship and knowing there were prisoners still alive there that he couldn't save frustrated and sickened him. Finding out that there could be as many as sixty Wraith hive ships making their way to our corner of the galaxy was a mixed blessing – to know what we were up against but also to know that at this point we really didn't have a way to defeat them.

Even their visit to M5S-224 had a disturbing element, despite the fact that it had taken place mostly within their minds. To go home only to find it was all a dream would have been so disappointing but at the same time to believe for just a little while that you were home must have been wonderful. Teyla shared her journey through Major Sheppard's eyes and took delight in telling me about her trip and how much she had enjoyed 'shopping'. Major Sheppard only said the experience was deeply disturbing, the sight of Teyla searching for hours for one outfit maybe only slightly less so than shooting Lt Ford or seeing friends he knew to be long dead.

I wondered how they did it sometimes – kept putting themselves out there only to be disappointed by their lack of success in finding allies or weapons we could use against the Wraith. I was glad my role on Atlantis was a lot lower key – apart from my brush with the shadow entity I had been kept well clear of the multitude of dangers that seemed to exist in the Pegasus Galaxy. When I heard a few days later that Major Sheppard and Teyla had discovered a huge storm heading straight for Atlantis I realised my safe run might be at an end.

Authors Note: Sorry this chapter was a bit disjointed ... didn't want to split it up and make two short chapters out of it.


	15. What the hell are you still doing here?

Authors Note: Warning ... this chapter contains some sexual references ... and some violence ... nothing strong though ...

**Chapter 15: What the hell are you still doing here?**

It's amazing how a grim situation can permeate even to the lowest levels of an organisation. Although I wasn't privy to every detail about the storm or what was being done to address the problems it would cause I could sense straight away the change that came over Atlantis. Very quickly the plan came down from Dr Weir's office that all the non essential staff would be evacuated to wait out the storm with the Manarans.

I was pretty sure that a stowaway would be considered extremely non essential. I don't know why but for some reason I really didn't want to leave Atlantis. Maybe deep down I was still worried that if I did they'd never let me back in. Major Sheppard had shown me the jumper bay a while back and I decided that one of the puddle jumpers would make an excellent hiding place to ride out the storm. I had the ATA gene and was confident I could raise the shields if I needed to. Major Sheppard would no doubt check at some stage to make sure I'd evacuated but I was counting on the confusion with the number of groups going through the gate to make it easy for him to assume I was gone. I knew they'd scan the city to be sure no one had been left behind but they wouldn't find me in the puddle jumper.

McKay and Zelenka came through with a plan that involved utilising the lightning rods by opening all the grounding stations. The power from lightning strikes would be collected and then directed through the very floors of Atlantis to power the shield. The last of the groups had been evacuated by the time the storm was less than 5 hours away. Teyla, Beckett, Ford and a group of Athosians were on their way back from the Mainland and would have to be evacuated when they got back.

After about half an hour inside the jumper I was startled from my thoughts by the sight of two men I didn't recognise. They were dressed in uniforms I knew weren't from Earth and carrying guns. I watched as they separated, clearly checking out the jumper bay and counting the number of ships we had. When I saw one heading straight for my position instinct and 3 months of basic training took over. Choosing my position carefully I waited quietly until just the right moment to strike out. Although he was bigger than me, the element of surprise allowed me to disarm him quickly and then render him unconscious with a well aimed blow to the back of the head. Unfortunately the noise he made when he fell to the ground drew the attention of the other soldier. He came running over, gun raised to fire at me. Before he could, I raised the gun I'd appropriated from the first guy, firing quickly and accurately just like I had in target practice. I ran to check his pulse and found that he was dead ... I felt a queasy sensation in the pit of my stomach as I started to come down from the adrenalin high. Steeling myself I dragged his lifeless body into one of the other jumpers. Finding some things to restrain the first soldier I dragged him to the other jumper too – bound and gagged and hopefully out for a few more hours to come. I went back to my puddle jumper and sat down shakily in the pilot's chair. Bringing up the control room HUD I could find nothing to explain the presence of those enemy soldiers. Searching around I found a spare radio and decided it was worth the risk to try to contact someone.

"John?" I whispered softly into the radio.

"_Sabina?_" Major Sheppard's incredulous voice whispered urgently back at me. I knew he'd be angry but I still felt a huge sense of relief to hear his voice. "What the hell are you still doing here?"

"No time for that," I ignored the question. "There are enemy soldiers in the city."

"It's the Genii," he said bitingly. "They've got McKay and Weir hostage. Where are you?"

"I'm in the jumper bay ... I had to um ... take two of them out," I admitted sickly.

"_What!_" the Majors voice was a heated whisper this time. There was a pause during which I resolved my best move was to say nothing. "Are you okay?" he asked in a calmer voice.

"Yes," I said reassuringly. "All that training must have paid off. What do you want me to do now?"

"Stay in the jumper until I come get you," Sheppard ordered me. "Don't do _anything_! And maintain radio silence!" That was the voice of 'Major Sheppard military leader', not my friend, so I knew the situation was grim. I followed his orders without question.

It made me uncomfortable to sit there doing nothing while he was out there facing danger, but then I came up with an idea that might possibly work. I assumed the Genii would be trying to track him with the sensors – maybe I could block his signature much like I did my own so that he could move around freely. I tried hard for some time but I didn't have much success. I couldn't maintain control with Sheppard moving too much and too quickly for me to keep up. With practice I could probably do better but for now I would have to be physically with him to pull it off and I knew he wouldn't go for that. I resigned myself to the fact that there was nothing else I could do to help.

I'd been sitting there contemplating my act of murder and worrying about the Major for a while when Jumper Two returned carrying Lieutenant Ford, Teyla and Dr Beckett. I was so relieved to see them, even though Ford refused to let me join them to help Major Sheppard. "The Major would have me for breakfast before demoting me back to private if I let you come," were his words when I asked.

So I sat there for what seemed like a very long time until Dr McKay's words came through the radio telling me he was activating the shield and that I should activate the jumper shields and hold tight. It all went as he'd planned, proving once again that he really was the smartest person on Atlantis.

I found out later everything that had gone on, how brave Rodney had been at the end, and how Major Sheppard had almost singlehandedly taken out the bulk of the Genii force, including killing who knew how many when he closed the iris on an open wormhole while Genii reinforcements were coming through. He was a military man who I assumed had killed enemy soldiers before - now I knew firsthand how dangerous he could be in protecting his people and the city.

It was just another piece in the puzzle I'd been trying to solve. Clearly Major Sheppard was both smarter and much more deadly than his demeanour would suggest. He was a strong and confident leader of Atlantis who really should have been above personal concerns - why the hell was he bothering with me? Sure, everyone needs a release but if it was just that then once I'd shown myself to be unwilling to have a casual fling, he should have moved on. I resolved that no matter how embarrassing it might be, I would have to talk to Dr Beckett because I had a sick feeling that the ATA gene had something to do with it.

Rather than gather with the others as they waited for everyone to return to Atlantis, I retired to my room to try and assimilate the events of the day. I had killed ... something I never thought I would even contemplate and it bothered me on a number of levels. I was so tired and yet I couldn't seem to relax my brain enough to sleep. I was lying there staring up at the ceiling, tears silently running into my hair when the door to my room opened. I didn't remember letting go of my hold on the door controls but maybe I was more exhausted than I had realised.

I turned away from the open door because I knew who it would be and I couldn't bear for him to see me upset. He didn't say anything, just silently made his way to my bed, lying down next to me and gathering me up so that he was spooned behind me. That made the tears come harder and I couldn't resist turning and burying my head in his chest, letting the tears wash away my conscious thought. I began to speak softly – somehow telling him what I had done in the dark was much easier than it would have been if I'd had to watch his reaction.

"It's okay," he reassured me. "This very situation was one of the reasons for training everyone in basic combat skills. You did what you had to do to defend yourself and I'm glad that it was them and not you. You need to put this out of your mind and accept it as something you can't change."

I nodded, knowing he was right. He hugged me tight once more and again I felt the tears come – this time they felt more healing than guilty. Eventually I must have wound down to the point of exhaustion because when next I opened my eyes there was daylight streaming through the windows, illuminating the eyes of John Sheppard as he lay next to me, watching me sleep.

"Morning," he said softly, tightening his hold on me like he knew I'd just been about to jump from the bed.

"Um ... morning?" I said it more like a question than a return greeting. "What time is it?"

"Still early," Major Sheppard replied. "Teyla turned up for your morning training but I told her you needed to sleep. She wants to talk to you later."

"Teyla _saw_ you here with me?" I asked with dread.

"She's not going to go posting it up on the commissary notice board you know!" he retorted. "Your reputation is safe for another day."

"Ha Ha," I said, while in my head a light bulb had gone off. I'd spent some time last night worrying that somehow the ATA gene was 'making' him pursue me but maybe it was much simpler than that. Maybe he was just so competitive in nature that my refusal to give in to what we both knew was there between us had made this a kind of game for him. He was the hunter and I was the prey. Maybe if he 'caught' the prey, the challenge would be satisfied and then he'd move on so we could go back to being friends. And yes I am aware of how naive it was to think I could sleep with the guy and then just go back to being friends like it never happened. I know I was fooling myself too that I could go the full distance with him and not walk away damaged when it ended but at the time I just didn't have the strength to resist anymore.

I looked at his tousled hair, his beard darkened face and then into his beautiful hazel eyes. And then I smiled. He was the one who looked worried as I leant forward and gently placed my lips against his.

"Sabina, what are you doing?" he pulled away to question me.

"Well if you have to ask then I'm obviously not doing this right!" I replied, moving in to kiss him again. He laughed weakly but I could tell that his instinct to question my sudden turn about was being swamped by his instinct to get me naked while he had the chance. Giving in, he took command of the kiss, moving us straight into a heated embrace.

It was those other times between us all over again, burning passion overriding sensible thought. It was almost a duel between us as we each strained to get closer, feel more, give more. This time there were no radios to interrupt us and no scruples on John's part that somehow this was all happening too fast. Events ran their course without pause for breath until that moment when we became one when we both stilled almost in shock.

I don't know if I can describe the connection I felt that was far beyond the mere physical to have John's body joined with my own. It was all the jolts of energy I'd felt at his every little touch multiplied by a million and then dispersed throughout my entire body. Before I could think any more he began to move and I was carried along on the tide of a passion like I'd never experienced. I could feel the climax building in every part of my body and when John surged forward and took us both over the edge I could not tell where he began and I finished.

Exhausted, we collapsed back onto the bed and just lay there together. John's hand rested on my naked back and his thumb absently stroked my skin, soothing me into sleep.

Authors Note: I tried to stay as close to what actually happened in these episodes as I could, while also making a place for my character, which I hope worked okay. This is the last bit of fluff there'll be for a while too so if that's been annoying you then you can keep reading!

Just as an aside "The Eye" contains one of my all time favourite Rodney lines "I'm an extremely arrogant man who tends to believe that all his plans will work."


	16. She came here because of you!

**Chapter 16: She came here because of you!**

Now that I had let myself be seduced into being with John Sheppard I wondered why I had protested so much. It got around the base apparently within hours that we were together, aided by the fact that John seemed to need to maintain some kind of physical contact whenever we were out together. After some initial comments and a fair bit of ribbing from our friends, interest in us just died. Clearly it was more fun to speculate about who might be with whom – once the speculation had turned into fact it was no longer interesting. In fact, everyone got used to me being a part of John's life with surprising ease. I resolved to relax and enjoy it, and to ignore that voice now buried somewhere deep at the back of my mind warning me this was too good to be true.

I'd always worried when I knew Major Sheppard was out on a mission but it was different now as I felt all eyes on me in concern whenever his team was late returning. I waited anxiously when John and Dr McKay failed to return from a scouting mission and hovered just as anxiously when John came back with a gunshot wound and a mass of bruises. "I know it looks bad," he said painfully when I went to visit him in the infirmary, "but you should see the other guy!" It was Dr McKay who told me it was a lone Wraith who had killed the other two members of their mission, and how close he and John had both come to being fed upon.

In fact, worrying about John Sheppard seemed to be turning into my second job. One afternoon I was studying in my room when Dr Weir's voice came over the city wide communications system.

"May I have everyone's attention please? We have run into a questionable medical situation and at Dr Beckett's suggestion we have decided to put the city into a self-regulated quarantine. For at least the next couple of hours, I need everyone to stay where they are, and report anyone moving freely through the halls. I hope you'll understand. Thank you."

Before I could even think of putting in my own call, John's voice came from the radio he'd insisted I carry at all times.

"Where are you Sabina?" he questioned, his voice sounding somewhat frustrated.

"My quarters," I replied. "You?"

"Stuck in the gym with Teyla," he growled. "Dr Weir won't let us leave."

"It is a medical quarantine John," I pointed out. "Not much the military can do about that."

"I know," he admitted. "But I'm gonna go crazy in here wondering what's going on."

"I'm sure Dr Weir will keep you up to date," I said, knowing him well enough to appreciate how frustrating he would find not being able to act. "Please don't do anything stupid."

"Me, do something stupid? When has that ever happened?" he quipped before getting serious again. "Look, I have to check back in with Dr Weir – stay in your room until you hear that the quarantine has been lifted."

"Okay," I said before he signed off. Putting the radio down I worried about what John would do if he had to spend too much time stuck in that lab. And sure enough, he admitted later that he'd defied the quarantine so he could go after Peterson, putting the whole city at risk and undermining Dr Weir's authority in the process. I was upset when he told me he'd taken a jumper out so he could drop of a nuclear bomb to take out the nanite virus – as much because of the risk to him as because he hadn't taken the time to contact me before he did it. I knew there would be many situations when he'd put the city before his relationship with me and that I would have to get used to it if I wanted to continue to be with him.

Then one day John returned from a routine mission with a beautiful alien woman and a look of utter captivation on his face. _"I TOLD YOU SO!"_ the voice in my head was screaming. When John didn't come in search of me as he usually did after a mission I felt darkness come over my heart. It seemed my time of belonging with Major Sheppard was already over after a few short weeks.

The humiliation of being completely ignored by Major Sheppard was only slightly worse than the humiliation I felt when Teyla, Ford and Rodney gathered around me with pity in their eyes. Teyla tried to excuse John's behaviour by telling me Chaya's planet had a weapon of unrivalled power that could defeat Wraith ships in space and that John would do anything to secure it or a place for as many refugees from the Wraith as he could. Rodney took a different tact, telling me how suspicious he thought Chaya to be and how he wouldn't be surprised if she'd put some kind of alien hypnosis on Sheppard to make him act that way. He said he'd prove it and then everything would be back to the way it was. Ford just patted my hand as if to tell me it would all be alright in the end.

When it turned out that Chaya was actually the ancient Athar, exiled from the ascended ancients because she had interfered with beings beneath her, it only seemed to make things worse. She went back to her planet and Major Sheppard of course returned to Atlantis. I retreated back into that defensive place I had been in before the storm changed everything.

"SABINA, OPEN THE DOOR!" I could hear Major Sheppard yelling at me from the hallway. "I'M GONNA STAND OUT HERE ALL NIGHT UNTIL YOU LET ME IN!"

"What can I do for you Major?" I asked in my chilliest voice, standing in my open doorway in an attempt to stop him from coming in.

"We need to talk about what happened," Sheppard replied, muscling past me and swiping the door closed on his way through.

"You don't owe me anything Major," I countered. "We never made any promises to each other – you're quite free to sleep or meld or whatever the hell it is you did with anyone you want."

"It wasn't like that," he protested. "She was an ancient – there was just something about her and even though I knew I should tone it back a bit I just couldn't seem to do it. She just wanted to learn more about our cultures and for all I knew she had a planet we could send everyone to for protection!"

"She came here because of you!" I retorted – I'd questioned Rodney mercilessly until he'd caved and told me the whole story.

"Okay, she said that, but it wasn't like what I have with you," he tried to excuse his behaviour.

"Well I guess I don't have as many ancient genes as she does, given that _she's_ fully ancient!" I hurled that one at him.

"What's that supposed to mean?" John's question was laced with the frustration he was feeling.

"You work it out Major," I almost taunted him. "Just do it somewhere else because right now I really don't even want to look at you."

"Sabina?" he almost pleaded, more than I would have expected from someone I knew would never beg for anything. "I didn't cheat on you ... I never intended to cheat on you."

"Not with your body maybe," I agreed. "But we both know you cheated on me in your mind, and you know what? I think I'd have preferred it if you had just screwed her." This time my voice echoed with the sadness I was feeling – I'd gone over and over this in my head trying to put a different spin on it but I just couldn't. My trust was broken and I didn't think I'd ever get it back and right then all I wanted was for John to just leave me alone.

I felt him come up behind me and I knew he was about to put his hands on my shoulders. Without thinking I shot an elbow out behind me and had the satisfaction of hearing his breath whoosh out as he grunted with the unexpected pain.

"This was the reason why I didn't want to get involved with you in the first place," I said quietly. "I _knew_ this would happen."

"You knew an ascended Ancient would come to Atlantis? Sheppard asked with a confused look.

"_NO_," I growled. "I knew that you'd move on when something ... better came along. We were never more than two people capable of really hot sex," I said those callous words without looking at him. "I'm sure both of us will be able to find that ... outlet ... with someone else."

"It was more than sex and you know it!" Major Sheppard straightened and moved towards me again, daring me to look at him directly.

"Maybe, " I said. "Maybe not. Maybe it wasn't even about us at all." I could tell that what I was saying was confusing him but I had no intention of explaining myself further. "Now I'd like you to leave – I will call security to come down and remove you and we both know how awkward that would be."

"Okay, clearly you need time to calm down and think about this rationally," he excused all my comments as though they were just a symptom of the anger I felt towards him. He didn't seem to see that I was well past anger and into resignation. "I'll leave quietly, so long as you agree that we can talk about this again in the future."

"Sure," I agreed easily. I knew that no amount of talking was ever going to fix what had been broken inside me.

With relief, Major Sheppard left me to my thoughts. Rather than dwell any more on how miserable he'd made me I turned back to my ancient lessons. I'd been neglecting them and my desire to read the ancient palm pad during my brief sojourn as Major Sheppard's girlfriend. It was time to refocus.


	17. Maybe you could turn it off somehow

**Chapter 17: Maybe you could turn it off somehow**

Saying you're going to do something and then actually doing it can be two very different things. I had every intention of carrying on as I had before I'd made the mistake of sleeping with Major Sheppard but inside I just felt so miserable and I missed him so much – even though I was still both angry and disappointed in him.

I pretended that I was fine with everyone but inside I was tormented. I couldn't sleep and I'd lost what little interest I'd had in food, helped by the fact that it was easier to just skip meals than have to sit there pretending I was enjoying myself when I just wasn't. I couldn't help but wonder too what people where thinking as I sat there so clearly no longer in the Major's favour. I went back to avoiding Sheppard and when I couldn't do that, I just refused to talk to him.

The only thing that seemed to take my mind off things was my studies and so I pursued them almost to the point of obsession. I was making quick progress and started to feel that it would not be long before I'd be able to make some headway in understanding the ancient palm pad.

"She won't talk to me Elizabeth!" I heard Major Sheppard's frustrated comment as I was coming up to Dr Weir's office to discuss some ancient symbols I was having trouble with.

"What did you expect John?" Dr Weir's voice came back to me sounding almost incredulous. "Sabina doesn't strike me as the type to trust easily and the fact that she trusted _you_ after so little time must make this even harder for her. You broke that trust ..."

"But I didn't _do_ anything!" John protested. "Nothing that was real anyway."

"John, this isn't about what _you_ think happened," Dr Weir counselled him now. "It's about what _Sabina_ thinks happened."

"I really care about her Elizabeth," John's voice had gone all quiet so that I could hardly hear him. "I don't know what I was thinking with Chaya but I never meant it to _be_ anything."

"You have to give Sabina time," Dr Weir said. "Step back a little and let her find her balance here again."

"I know," John said it grudgingly. "But I really really hate this – we all know how completely I suck at the whole talking about my feelings thing. I need action ..."

I decided I'd heard enough and turned away before I could hear the rest of that statement. I'd been ignoring the need before but now I felt it was time to go and talk to Dr Beckett, embarrassing as it was going to be. Even more so than it would have been if I'd spoken to him when I first thought of it. Knowing that Sheppard was occupied with Dr Weir I decided there was no time like the present.

"Ah ... Dr Becket?" I called out as I entered the infirmary.

"Hello lass,' he greeted me. "What can I do for you today?"

"Can we talk privately?" I almost whispered.

"Of course lass, come into my office." Dr Beckett put a guiding hand on my shoulder and led me towards his office.

Once there I sat and then just looked at him, trying to work out how I was going to do this.

"Just spit it out girl," he advised. "I won't be judging you."

"I know – I'm just not sure where to begin." I hedged, chewing nervously on my bottom lip. "Okay, first off I should tell you that I know about those mutant genes you found when you did my initial blood work – I heard you and Dr Weir talking about it."

"I know Sabina," he said, putting a wonderful Scottish lilt on my name. "Major Sheppard told me ages ago."

"Oh," I said, momentarily speechless by that. I didn't know Sheppard had talked to the Dr about me.

"If this is about those genes, you've got nothing to worry about. Just because I haven't worked out their purpose doesn't mean they're dangerous and it certainly doesn't make them mutant.'"

"It's not about them," I discounted that before thinking some more. "Well it is about them but only in a roundabout way. Do you think there could be some genetic imperative for those with the ancient gene to be drawn to each other?" I rushed the question out and almost cringed waiting for his reply.

"Why do you ask?" Dr Beckett's voice was intrigued.

"Well, I'm sure you know that Major Sheppard and I were ... intimate for a time," I almost mumbled that one, face flaming as I looked anywhere but at the Dr. "It was really intense – the um ... sex ... I mean ... it was really _really_ intense and I was thinking about it because that can't be natural right? I mean why would the Major be interested in ... why would he be compelled to do anything of a personal nature when he's got such an important professional role here. And look what happened with Chaya – John said he couldn't seem to pull back from her and she was brimming with ancient genes. Of everyone on that mission it was John she was drawn to ... I mean he is very attractive but what if it wasn't just that? And so I thought that maybe it was the ATA gene trying to make us get together to preserve the gene ... you know ... how else would it still be around almost 10,000 years after the ancients ascended?" My words ground to a halt and I wondered if I could possibly be any more embarrassed.

Dr Beckett was silent as he tried to sort through the jumble of what I'd just told him.

"Because if that's the case I thought maybe you could turn it off somehow because I really don't want to go on like this!" I continued without waiting for his response, feeling on the very edge of tears.

"Oh lass," he said gently. "I'm sorry you're having such a hard time of it right now." He put a hand on my shoulder in an attempt to comfort me – I was so miserable I hardly even noticed the usual jolt I got from his touch. "There's really no evidence to suggest the ancient gene does anything like you're describing," he began.

"Well, maybe it's the ancient gene plus those other ones," I said, unwilling to hear that there was no connection between the genes and the way I'd been feeling.

"Have you felt anything similar with anyone else here who has the gene? Dr Beckett asked gently.

"Well you know," I hedged, getting embarrassed again. "Not as strong as Major Sheppard but I do get a jolt when people who have the gene naturally touch me."

"You never said anything," Dr Beckett scolded me.

"I didn't make the connection at first because there aren't that many people here who already had the gene. I just thought it was because you and the Major were just really good looking." I tried to make a joke and was relieved when Dr Beckett chuckled. "After a few weeks I just avoided touching anyone so it wasn't an issue and I pretty much forgot about it."

"Well I can run some tests if you feel that strongly about it but I'm not sure what I'll find," Dr Beckett suggested. "Even if I could, I wouldn't advise turning off any genes because I don't know what the effect of that would be."

"Oh," I was disappointed that it wouldn't be that easy. "Okay then, well thanks for listening," I was very eager to leave Dr Beckett's office right about then.

"You know Sabina," I paused to hear what he was going to say. "When two people love each other sexual intimacy can be as intense as you've described."

"John doesn't love me," I said in a quiet, sure voice.

"But you love him," Dr Beckett said it like there was no room for denial.

"Let me know if you find out anything," I requested in a trembling voice before I bolted out the door.

Authors Note: Sorry if this is a little on the fluff side ... it's the last of this sort of thing for a while ... next chapter gets into the palm pad in more detail.

Thanks to EmSyd and PinkBug for my very first reviews ever! I'll keep doing the chapter (or more per day) update until this is all finished. I've got vague thoughts of changing a few things but nothing too major.


	18. Everything you need is in the room

**Chapter 18: Everything you need is in the room.**

We found Elizabeth - not our Dr Weir but an Elizabeth who had gone back 10,000 years and then travelled forward to ensure that Atlantis wouldn't fall to the sea. I was staggered by that kind of sacrifice and wondered if there was any chance that I'd get to talk to her myself.

It had been a couple of weeks since I'd talked to Dr Beckett and things had settled as much as I expected them to. Major Sheppard and I had reached a truce of sorts once he'd accepted that while I was no longer avoiding him I had no intention of reforming our previous relationship. I greeted him as I had when we were just friends while refusing to talk more about the Chaya incident whenever he tried to bring it up. He gave the appearance of having given up on us as a couple – it was what I had wanted but knowing that he had done so only made me that much sadder.

I was still not sleeping well ... troubled within myself as though an essential part of me was missing. Surely I had not gotten that used to having John around that I could no longer sleep without his presence?

When I did get to sleep strange dreams plagued me – in some I was surrounded by ancient symbols I couldn't understand and in others I was walking down the corridors of Atlantis searching for something.

Still, the extra time to study had ensured that I was now able to read most of what was on the palm pad. Read it but not exactly understand it. From what I could tell it was talking about a special room located somewhere within the bowels of Atlantis that was only operated by just a handful of the original ancients. This was where those 'mutant' genes I had asked to find out about came in.

The technology in the special room, much like that in the rest of Atlantis, had been designed to ensure that it couldn't be operated if Atlantis fell into the hands of an enemy. I couldn't understand what the room had been designed to do though – 'send forth the repelling breath upon the enemy and bring healing to the galaxy' was as close as I could get to a translation. I had the sense that the room was dangerous, more so than other ancient machines we'd found reference too, which is perhaps why only a small subset of the ancients were able to operate it. I'm not sure if they engineered the extra "ancient" genes or if they took advantage of an evolutionary difference that was already there.

I really wanted to talk to 10,000 year old Elizabeth so I could ask her myself. Imagine my excitement when Dr Beckett called me to tell me ancient Elizabeth had asked for me.

"Elizabeth?" I asked softly, walking quietly towards her bed.

She had looked to be sleeping but at my approach she opened her eyes and smiled in recognition.

"Sabina?" her voice was that of an old lady but at the same time held hints of the Elizabeth I knew.

"Dr Beckett said you wanted to see me," I queried.

"Yes child," she held out a wrinkled hand to draw me nearer.

I sat beside her bed as she began to speak. She told me that I'd been there that first time Atlantis fell and that although she hadn't known me well, events had happened during her time with the Ancients that had made her realise how important I would be to the Atlantis mission. I was about to question her further but was shocked into silence by her next question.

"Have you found the room yet?" She asked.

"No, I only just succeeded in translating most of the text," I admitted, knowing immediately what she was talking about and looking around to make sure no one could overhear us.

"You must hurry," she urged me. "10,000 years ago the ancients were reluctant to make use of the weapon once it was completed. They thought they had time to come up with another solution but they didn't protect the only ones who could use it until their very numbers were threatened. They let things get too far until the Wraith inhabited every corner of this galaxy. Believing they could find a solution if they had time they retreated to Earth, taking the last of those special ones with them."

"And never got the chance to come back," I commented softly.

"Yes. Janus believed that the time would come when we would return to Atlantis and make use of the weapon. He researched the problem until the very last moment when he was forced to abandon his work – his notes are on that palm pad you discovered. Rodney should be able to make use of Janus's research but it falls to you to learn how to operate the weapon itself. Everything you need is in the room with the weapon."

"But where is this room, Elizabeth?" I asked hurriedly.

"The city itself will show you when you are ready Sabina," Elizabeth's eyes drifted closed and I knew she had fallen into sleep.

I sat there for some time thinking about what she had said, until Dr Beckett returned and urged me to get some sleep. I don't know why I chose not to confide in anyone – at the very least Dr McKay could have helped me decipher the more technical aspects of what was on the palm pad. I just felt that this was my mission here on Atlantis – this was the reason why I had ended up here against all the odds. It was for me to solve the puzzle, and I didn't want that taken away by people who were no doubt more qualified than me. It was selfish and I would probably regret it later, but just this once I didn't want to be the dummy who was brought in at the last minute to put my hand on something without being required to understand why I was doing it.

Ancient Elizabeth completed her story and not too long after slipped into her final sleep. I don't know how our Dr Weir felt about that - I was saddened at her passing but happy that she had gotten to see that the sacrifice of her entire life had not been in vain.


	19. Anything else you haven’t told me?

**Chapter 19: Is there anything else you haven't told me?**

Now that I knew I was really on to something I spent even more time obsessing over the palm pad. I also began to disappear for hours every day, walking the corridors of Atlantis as yet unexplored, looking for clues to the rooms' location. I know Ancient Elizabeth had said Atlantis itself would show me when I was ready to find it but I didn't trust that this could be true.

I wanted to see if Dr Beckett had learned anything about the ancient genes yet so I made my way to the infirmary one day a few weeks after ancient Elizabeth had been found.

"I'm worried about her Major Sheppard," I heard Dr Beckett's concerned voice. "She's not sleeping well and she's lost weight – she's running herself into the ground."

"What do you think I can do about it Carson?" Sheppard was obviously frustrated. "She won't listen to me."

"Have ye tried lad?" Dr Beckett didn't give up. "Sabina cares about you – cares about your opinion. I'm sure if you tried you could get her to ease off a bit."

Wasn't it amazing how much you could learn on Atlantis just by keeping your ears open? Eavesdropping sounded like such a nasty thing to do but honestly they were all so oblivious to the people around them that I didn't even have to try. Deciding they'd had more than enough time to talk about me I cleared my throat loudly and almost stamped my way into the room.

The atmosphere made it obvious that Sheppard and Dr Beckett had been talking and had shut up just moments before I'd arrived so hopefully they weren't aware that I'd overheard them. It would be interesting to see whether Major Sheppard actually did try to talk to me about my work and sleep habits.

"Hi Dr Beckett, Major" I greeted them innocently. "I was just wondering Dr Beckett if you've made any progress on that ... problem we discussed a while back?"

"Not yet lass," he admitted, "although to be honest I haven't had much time so far."

"That's okay," I excused him. "It's probably not as important now anyway. Well, I've got lots of studying to do so I'll see you both later." I turned to exit the room, not missing the significant look Dr Beckett shot at Major Sheppard. I saw Sheppard roll his eyes before reluctantly following me out of the room.

"Hey Scotty," he called out. "Wait up!"

"Major," I acknowledged. "Was there something you wanted?"

"There you go with that question again," he almost teased me and I had a sudden memory of his response last time I'd asked him something like that.

"Ha ha," I tried to shrug it off. "You called out to me remember – why?"

"Oh, well I just wanted to talk to you about ... um ... Dr Beckett was worried about ... look, have you got a few minutes for a drink? I need to sit down for this one." Sheppard stumbled his way through, giving me that adorable lost puppy dog look he sometimes used to charm his way through something.

"Oh all right," I conceded. "But this better be good."

Instead of taking me to the commissary the Major grabbed a couple of water bottles and kept moving through the city until we came to an unused balcony. I couldn't help but wonder if this was the one he'd taken Chaya on a picnic to.

"No I _didn't_ bring Chaya here," he said in an almost insulted tone, sitting down on the only bench available.

"How did you know I was thinking that?" I protested.

"Because I know you Scotty and I could almost see the question written across your forehead!" Sheppard shifted uncomfortably. "Would you sit down already?"

I sat down without a word, taking the bottle he offered me and gulping it down quickly.

"Dr Beckett's worried about you," Sheppard began. "And to be honest so am I."

"I'm fine," I denied any need for them to worry.

"No you're not!" Sheppard looked at me closely. "Have you looked at yourself lately? You've got dark circles under your eyes, you've lost a lot of weight and you hardly talk to anyone these days unless it's about whatever project you're working on."

"You make me swoon with all these compliments Major," I tried again to deflect his attention.

"You need to take this seriously!" Suddenly I was talking to the very daunting Major Sheppard, the one in charge who wouldn't hesitate to do whatever it took to protect his people. "And you need to come clean with me about what you've been working on because I know it's not training anymore. Elizabeth says you're as good as she is these days at translating ancient. You disappear for hours on end and we can't find you because you always blank yourself off the sensors. Something's going on and I'm tired of waiting for you to tell me what it is."

"_Nothing's_ going on!" I denied but like that day so many months ago I couldn't maintain my eye contact and quickly looked down before he could see I was lying.

"Sure, nothing," he said almost sadly. "I knew I should have confronted you weeks ago when I first suspected something was off."

"Why didn't you then?" I asked, curious despite my nervousness that it would all get taken away from me.

"Because I was still tiptoeing around you over the whole Chaya thing and I didn't want to do anything else to piss you off! I _trusted_ you to tell me if there was something going on that I needed to know about," he explained.

"You're right," I reluctantly agreed. "I should have told you as the military leader of this expedition. I'm sorry – I was so caught up in my personal ... concerns ... I just haven't been thinking straight." The game was up – I had to let him in and hope it didn't end up with me being pushed out into the cold.

"So tell me," he invited.

"It's better if I show you," I replied. "Come on." Jumping up I headed for my quarters without looking back, trusting that he'd be right behind me.

Once we were both inside I walked over to my concealed wall safe and waved my hand over it. Major Sheppard gave a small whistle as the panel disappeared to reveal the space within. I took out the palm pad and silently handed it to him. Of course it lit up as soon as he touched it.

"_This_ is why you wanted to learn ancient?" he asked with an angry edge to his voice. "You've had this thing the _whole time_ since before we were together and you never told me?!"

"Yes," I admitted miserably. I wasn't surprised that he had so quickly worked out my motives and deduced I'd been keeping this secret for a lot longer than he'd originally thought.

"I didn't know it meant anything to start with," I tried to excuse myself. "I thought it was just going to be about my ATA gene. By the time I realised, things were all weird between us and I just ... I don't know!"

"Is there anything else you haven't told me?" he asked, still seething with anger.

I had worried that he would let his relationship with me get in the way of his duty but I saw then that it was in fact me who had done that. If I didn't have all these seething emotions swirling inside me I'm sure I would have come to him with the ancient palm pad the day I found it. I deserved his anger ... and I still had to tell him what ancient Elizabeth had said.

"Ancient Elizabeth knew about the palm pad," I admitted miserably, sinking down onto my bed and looking away from him. "Janus left it for us to find."

"Oh this just gets better and _better_," he said in an annoyed tone, before turning away and rubbing his forehead in frustration.

"Okay, just tell me all of it," he commanded, sitting in a chair across from me and waiting expectantly for me to begin.

So I told him the whole story. He refrained from making any comments - when I got to the part about there possibly being a Wraith destroying weapon somewhere in the city I could see him clenching his teeth to stop himself from blasting me.

"Is that it?" he asked in that deadly quiet voice he's so good at.

"I still have that laptop you gave me before you knew I wasn't supposed to be here," I said, trying to lighten the mood, without success.

Silence descended on the room as he sat there looking at me, clearly thinking about all the implications.

"I can understand you keeping the palm pad to yourself to start with - you didn't know us and you were looking for your place here," he began. "But what I _can't_ understand is why you kept silent about the fact that there's a potential weapon somewhere in this city!" His voice was frustrated, and angry, and disappointed too. Strangely it was his disappointment in me that I found the hardest to deal with. "It's my responsibility to protect this city and everyone in it from the Wraith," he continued. "We need every advantage we can get and we need them yesterday!"

"I'm sorry," I whispered, struggling not to cry. "I let my emotions get in the way of doing my duty. I don't know what else to say ..."

"I'd cut you out of this if I could but from what ancient Elizabeth apparently said we need you to make it work. But let me tell you this," he leaned in and his voice was all intimidating and serious. "If I find out you've kept anything else from me, no matter how small, I'll bust you back to the brig so fast you won't know what hit you."

He got up and motioned for me to follow him. "We need to fill Elizabeth in."

Authors Note: Thanks again to PinkBug and EmSyd for the reviews ... hope you like these new chapters!


	20. Maybe I'm not ready

**Chapter 20: Maybe I'm not ready.**

Dr Weir was quiet while I miserably told the whole story to her. She didn't get angry like Major Sheppard had but I could see that she too was disappointed in me.

"Why would you keep this from us Sabina?" she asked quietly.

"Like I said to Major Sheppard," I began. "To start with I really thought it was just going to be a way for me to learn about my DNA - it was only recently that I found out it was much more than that."

"You should have said something then," Elizabeth admonished.

"I know," I agreed miserably. "But if I had then you'd have handed the whole thing over to someone much more qualified than me!" I finally admitted. "The palm pad was revealed to me - ancient Elizabeth asked to speak to _me_ - I wanted to do this, I needed to solve this to prove that I _do_ belong on Atlantis." I was painfully aware of Major Sheppard's silent presence in the room - I had no idea how he'd reacted to that last statement and I didn't really want to find out.

"Sabina," Dr Weir scolded me. "You _don't_ have to prove yourself! You have the ATA gene - if we'd found you on Earth we would have _asked_ you to join the mission."

"No you wouldn't," I disagreed. "The only people here who had the ATA gene naturally also have other qualifications. Carson is a talented doctor. The Major is in charge of the whole military angle. I don't have any qualifications. Well I didn't - that's one of the reasons why I was so keen to learn ancient."

"I'm sorry we didn't do a better job of making you feel secure here," Dr Weir said. "There's no point in dwelling on what's done - we need to work out a plan for how to proceed from here."

"Did ancient Elizabeth give you any clues to the rooms' location?" Major Sheppard spoke for the first time since we'd arrived at Dr Weir's office.

"Not really," I replied. "All she said was that the city itself would show me ... when I was ready."

"That's what you've been doing all those hours when you were off sensors - looking for the room?" He questioned me further. His voice sounded quite reasonable without any hint of the anger he'd shown me earlier but I knew it wouldn't be that easy for him to forgive me.

"Yes, and I haven't found anything." I admitted.

"Well, that's a starting point then," Dr Weir instructed. "Sit down with the Major and mark out on a map of Atlantis all the places you've already looked. We can put teams on searching the rest."

"I can do that,' I agreed. "But I'm starting to think I could have already walked past it without knowing it. I don't think walking around the city is the way to find it."

"What about the sensors?" Major Sheppard suggested. "You're pretty good at manipulating them to hide yourself ... could you tap into them somehow?"

"That's not a bad idea," I commented in surprise.

"Well I do have them occasionally," he said with a self depreciating smile.

"And it fits in with what ancient Elizabeth said ... it takes a fair amount of concentration so maybe she meant I'd be ready when I'd developed enough mental control." I felt excitement at the idea.

"Okay then," Dr Weir agreed, turning to the Major. "Talk to Rodney, get Sabina hooked into the sensor system and we'll take it from there. Let me know as soon as you find something."

"Why didn't you tell me you felt that way about not belonging on Atlantis?" Major Sheppard questioned me as we headed down to Rodney's lab.

"What could you have done about it?" I denied that I should have said anything. "When we were friends and I was doing basic training it just seemed like a weakness I should be able to overcome. Then we moved so quickly into ...," I blushed and looked down at the floor, "you know ... and then for a time I did feel like I belonged so it wasn't an issue anymore."

"And after?" Major Sheppard kept walking, me hurrying to keep up with his longer legs.

"I was angry ... more than I can remember ever being," I admitted. "I _know_ I should have told you about the weapon okay - I know - I let my personal feelings get in the way and pretty much proved that I _don't_ belong here."

"You had every right to be angry," he surprised me with that comment.

"No I didn't," I said with a frown. "You were free to behave in whatever manner you saw fit with Chaya. We'd hardly even begun our relationship and we didn't make promises... I said it at the time but it was only later when I truly believed it."

"So you forgave me?" he asked, stopping in the corridor to look at me. "Then why didn't you say something?"

"I did, in a roundabout way," I said, looking up at him reluctantly, "when I started talking to you again."

"Oh," he sighed. "So why aren't we ... you know?" His hand gestured a connection between us.

"You were right," I said, turning away to continue walking down the hall.

"I like that,' he smiled as he caught up with me. "What was I right about this time?"

"It was too fast and I did screw it up by rushing things," I admitted. "I just don't think I'm cut out for relationships ... I get too emotional and I can't seem to separate that from doing the job. It's not that I don't think personal relationships have a place on Atlantis because I do. The people here are so cut off and they need whatever comfort they can get."

"Just not you?" he queried with a frown.

"Right!" I agreed. "Just not me."

"Now isn't the time," the Major said as we arrived at Rodney's lab, "so I'll let that go. But we will be talking about how ridiculous that last comment was later."

I made a childish face at his back as I followed him into Dr McKay's lab.

Rodney was intrigued by the idea of using the sensors to find a room we knew was somewhere in Atlantis. I spent hours that day trying to get my brain to make a deeper connection with the Atlantis systems but it just wasn't working.

"Maybe I'm not ready," I commented tiredly to Major Sheppard, who'd stopped by to check on my progress, or lack thereof.

"Or maybe you're just tired,' he disagreed. "You've been pushing yourself for weeks and you look like crap."

"Be still my beating heart," I pretended to swoon with one hand on my chest and the other over my forehead.

"Funny," Sheppard said without laughing. He grabbed my hand and dragged me out of the room "Time for dinner," he ordered, pulling me with him in the direction of the commissary.

For the first time in ages I actually felt hungry and I didn't care if people were talking because the Major and I had turned up and sat together. Before I could finish a dizzy wave of almost unconsciousness fell over me and I would have fallen out of my chair if Sheppard hadn't caught me.

"Sabina!" he said urgently.

"I'm okay," I mumbled the excuse. "Just ... tired." And with that I leant my head against his chest and fell into sleep.

It was hours later when I woke up in my own bed. I stretched, feeling more refreshed than I had in too long. I looked around the room, wondering how long I'd been sleeping, and spotted Major Sheppard asleep on the chair across from me. Quietly I exited the bed and crept over to him. I couldn't help the tender smile that graced my face as I took in the picture he made with his face relaxed in sleep, hair sticking up in a dozen different directions. He was seriously cute. I should have known I couldn't creep up on an ex special ops soldier though - before I'd even realised he was awake his hand shot out and grabbed my arm, pulling me into him.

"Hey!" I protested.

"How are you feeling?" he pulled me onto his lap and ran his eyes across my face. "Carson said you were exhausted and we should just let you sleep it off."

"Wait, when did I see Carson?" I sat on his lap as though I did it every day, trying to show him that his nearness was having no effect on me.

"He came to the commissary after you fell asleep on me," Sheppard informed me. I fell asleep on him in the commissary during the peak dinner hour? Great!

"Oh, sorry about that," I apologised.

"No problem," he said lazily. "It was kinda nice actually - getting you to do what you're told without having to hear a whole bunch of arguments."

"Ha ha," I said, squirming a bit as I tried to sneak my way off his lap. "Are we all done here?"

"Not yet," Major Sheppard let me get up. He stood and did one of those full body stretches that showed off every muscle and raised his t-shirt to give me a tantalising view of his stomach. I looked away quickly but not before he caught me ogling him.

"We should get back to the lab," I said, turning away from him. "I'm close - I can feel it. I just need to concentrate harder."

"Sabina," his deep voice came from too close behind me.

"Not now," I pleaded. "I promise I'll sit and listen to whatever you want to say ... just later okay?"

"Okay," he agreed easily. Thinking he would move away I was surprised when he pulled my pony tail aside and placed a gentle kiss on my neck before leaning in and rubbing his face into my shoulder.

"Are we good?" I asked in a small voice.

"We're getting there,' Sheppard replied, not pretending he didn't know what I meant. "I'm still annoyed with you for keeping quiet about the weapon _but_ I didn't give you much reason to trust me, did I?"

"Thank you." I turned around and hugged him quickly before stepping away. "Time for work," I announced in a more cheerful voice.

"No,' Major Sheppard disagreed. "Time for breakfast ... _then_ it'll be time for work."

"Okay," I grumped. "I'll just go do the stuff we women do in the mornings - I'll be there in ten."

"I'll be waiting,' he promised.

Authors note: It's a given that the sensor system can't find a specific person BUT after The Eye we do know that lone sensor signals do stand out and that they would do checks of the city from time to time - Sabina would know this too hence hiding her signal. Rather than put in a big scene explaining all that, the story flowed better to just assume Sabina and John would have talked about it at some point.


	21. I just imagined a big blanket

**Chapter 21: I just imagined a big blanket and hid the two of us under it.**

I hoped that after more sleep and food than I'd had for a while I'd make some progress with the sensors but the whole morning was spent getting more and more frustrated.

"Why isn't this working?" I angrily pushed away from the ancient console.

"Don't give up," Dr McKay reassured me. "I mean the fact that you can block out the sensors the way you do is just amazing. Have you tried to do anything else like that?"

"Well, I tried to block Major Sheppard's signal when the Genii took over,' I admitted. "It worked for a few seconds I think but I couldn't maintain my control because Sheppard was moving too fast. I thought at the time that I'd have to be physically there with him to make it work but I haven't had the chance to test that out."

"Let's get Sheppard down here," Rodney suggested. "You're not making progress going straight at the problem - maybe this will help."

"Rodney," Major Sheppard complained as he arrived. "This better be good - I'm in the middle of planning our mission to Dagan.

"Oh right, one of the ZedPM planets from Ancient Elizabeth's list," Rodney nodded distractedly. "Well this won't take long and then you can get back to counting your ammo or whatever it is you do to plan a mission."

Although the comment was biting I knew that Sheppard and Rodney shared a strange but close friendship so I just smiled as Sheppard raised an eyebrow at me.

"I'm not making any progress," I admitted. "Rodney thinks if I do something else it might help. When the Genii took over I tried to block your sensor signal like I do my own. I thought I might be succeeding here and there but it was too hard because you were just moving around too damn fast."

"Okay, so you want to try that now?" he guessed why we'd called him down there.

"If you don't mind?' I acknowledged.

"What do I do?" he asked, stepping closer to me.

"Just stand still for now," I said distractedly, turning to Rodney and asking him to get the sensor map to display this room. Three life signs registered, then two as I put up my own block with the ease of much practice.

"That is so cool," Dr McKay breathed before registering my annoyance at his interruption. "Okay, now try to get rid of Major Sheppard's signal."

In my head I'd developed the method of spreading a mental blanket over myself as the trigger for hiding my signal. Now I tried to make the blanket bigger and spread it over Major Sheppard as well. As I watched a second life sign dimmed and then went out. I smiled in relief but it was short lived because as soon as I took my concentration off him for a second, Sheppard's signal reappeared.

"Damn," I grumbled.

"It's okay Sabina," Major Sheppard said, while at the same time Dr McKay said "Touch him!"

"What?" we both turned to Rodney.

"You have the gene, he has the gene. Maybe touching him will reduce the burden of hiding him? After all, he's always saying how much Atlantis likes him!" Rodney said in that voice he uses when he thinks something should be completely obvious.

"Oh, right" I commented, putting my hand on Major Sheppard's arm and trying again. This time it _was_ easier to keep my blanket over the both of us. No one said anything as I held the block for minutes. I was amazed at how quickly I found a way to put the block on both of us to the back of my mind and free up some of my mental capacity. When I was first learning the technique it had taken days to achieve the same thing for myself.

"What now?" I asked, noting that both of them looked impressed when I managed to hold the block while speaking to them.

"Can you do that if we move around a bit?" Major Sheppard tone suggested he could see the value of this from a tactical point of view.

"Shall we go for a walk and try it out?" I asked, turning to Rodney. "Can you let us know when Major Sheppard's life sign reappears?" I requested.

It was a little awkward walking with my hand on Sheppard's arm and we did get a few looks as we turned away from Rodney's lab and headed for the control room.

"How are you doing this?" Major Sheppard asked.

"I just imagined a big blanket and hid the two of us under it," I admitted reluctantly.

"Cosy," Sheppard grinned, clearly enjoying making me uncomfortable.

I had been expecting Rodney to tell us he could see Sheppard's signal but we made it to the control room with no word from him.

"McKay?" Sheppard barked into his radio. "Are you reading us?"

"Wouldn't I have said something if I was?" Rodney complained. "Where are you? Because I couldn't track you once you left the room. I can't tell your signal from anyone else's so I don't know if you're being picked up or not!"

"Oh right," Sheppard said quickly. "Well can you tell me how many people there are in the control room right now?"

"Two," Rodney said immediately.

"Sabina and I are both here so there should be four," Sheppard informed Rodney. "Not bad Sabina," he acknowledged.

"Take your hand off him," Rodney instructed me "but try to maintain your block."

I did what he said and waited to hear the result.

"Still only picking up two life signs," Rodney congratulated me. "How does it feel from your end?"

"I had to concentrate hard when I first let go," I said cautiously. "But now it doesn't feel that much harder than what I do for myself."

"Nice,' Sheppard commented. "What about if I'm not in the same room? This won't be much help if you have to be with me."

"Rodney?" I asked.

"Go for a walk Sheppard," Rodney's voice came back over the radio. 'But this time can you tell me where you're going? Do it quietly though because I don't want Sabina to hear you."

"Okay," Sheppard agreed readily, giving me a smile before he turned and left the room. I sat and concentrated on maintaining my link with the sensor system - my theory was that I didn't have to be with Sheppard because I now knew what his signal 'felt' like to Atlantis. I could find that feeling in the system and put a separate blanket over that. I started to shake a little at the effort I was putting in and eventually I had to let go.

"Sorry Rodney,' I apologised weakly. "I couldn't maintain it but with practice I probably could."

Overall we agreed it had been a successful morning. I was so tired I didn't even argue when Major Sheppard instructed me to have some lunch and take a nap.


	22. The room, it's not big enough

**Chapter 22: The room, it's not big enough.**

Despite my success with hiding Major Sheppard's sensor signal it was still a couple of days before I made the big breakthrough.

Sheppard had come to check on me, something he seemed to do at regular intervals every day. "How's it going?" he asked.

"This sucks!" I said angrily. "I _hate_ this console."

"No you don't," he said, giving my ponytail a light tug. "You're _obsessed_ with that console."

"I'm running out of ideas here," I admitted, looking up over my shoulder at him to complain. "This is really frustrating!" Turning back to the console I almost slammed my hands against it and yelled "SHOW ME THE WRAITH WEAPON ROOM, FOR GODS SAKE!"

As I'd started yelling, Major Sheppard had put a calming hand down firmly on my shoulder and at his touch I felt a huge surge of power. It definitely came from him, picking up speed and intensity as it travelled down my arm and into the console. It wasn't a physical thing - no one else in the room would have noticed anything, but the result was definitely spectacular. All the lights in the room went off but the console lit up so much the room was shrouded in that bright blue light the ancients liked so much. A map of the city appeared on the big screen, showing an area located down in the depths of Atlantis. One room was pulsing slowly, burning itself into my brain.

"Do you know where that is? I whispered to Sheppard.

"Yeah," he said, taking his hand off my shoulder. Immediately the display disappeared and the lights came back on.

"What did you do?" Rodney exclaimed.

"I didn't do it," I said quietly. "_He_ did!" and I turned to look accusingly at Major Sheppard.

"What?" he denied it. "I didn't _do_ anything! All I was thinking was that I wished I could help you somehow and then _you_ made the map appear."

"I didn't" I disagreed.

"Well I didn't either," Sheppard retorted.

"Okay children can we focus here?" Rodney cut in. "It doesn't really matter how you did it - we now have somewhere to look for the Wraith weapon room so how about we stop arguing and start moving?"

"You're right Rodney," Sheppard snapped into leader mode. "Elizabeth," he said into his radio. "We're heading down to the lower levels of Atlantis. We may have found Sabina's room."

"Acknowledged," Dr Weir replied. "Keep me informed on your progress ... and be careful."

"Will do," Sheppard replied before turning to me. "Shall we?"

It took some time to get there, even using the transporters, because it turned out the room was at the very bottom of Atlantis. As we walked along darkened corridors Atlantis itself seemed to welcome our passage, turning on just enough light for us to see ahead.

"I think we're on to something here," Rodney commented, consulting his data pad with a frown. "According to my readings, there's an empty shaft up ahead ... I'm pretty sure something like that was mentioned in that weapons research inventory Sabina activated. Of course the Ancients didn't bother putting in any details about where it was, but this could be it."

"Did the inventory happen to tell you what kind of weapon it was?" Major Sheppard asked, pointing his P90 around a corner before motioning us to continue.

"No," Rodney admitted. "I think most of the stuff on that inventory was extremely experimental and potentially dangerous ... they wouldn't have wanted details falling into the wrong hands."

"You do realise there's nothing between us and the ocean except this floor, right?" Rodney commented nervously a few minutes later. "I mean, its reinforced and it seems to be structurally sound but ..."

"_Rodney_," Major Sheppard interrupted the beginnings of a classic McKay tirade. "Let it go!"

I said nothing as I listened to their conversation. After we'd turned that last corner I had known we were close ... I felt a sense of recognition as well as expectation that was only heightened the closer we got to our destination.

"This is it," Rodney stopped at an innocent looking door. "That empty shaft is right above this room and it's huge. Take the ceiling away and we'd see the sky a _long_ way above us."

Major Sheppard swiped his hand over the door panel but nothing happened.

"Losing your touch Major?" Rodney smirked at John's surprised look.

"Sabina?" Sheppard motioned me forward. As soon as I put my hand near the door panel, the door slid open with a faint grinding sound.

Major Sheppard went in first, weapon at the ready, followed closely by Rodney. After a moment where I waited anxiously in the corridor Major Sheppard motioned me into the room.

I should have realised it wouldn't be as easy as walking down there and just opening the door. This room looked exactly like all the other lab's we'd found on Atlantis. The only problem was it was completely empty - it didn't even have all the consoles and equipment that usually went with them.

"You have _got_ to be kidding me!" I looked around in disbelief.

"Just wait,' Major Sheppard cautioned me. "Rodney, are you picking anything up?"

"I'm not getting any energy readings but there is something definitely not right about this room," Rodney replied distractedly, holding his sensor pad out in front of him as he walked around the room.

"It's not big enough," I said quietly.

"What?" Rodney turned back to me.

"The room, it's not big enough," I restated.

"How could you know that?" Rodney asked me curiously. "There weren't any dimensions on the map and nothing about its shape to give us any clues as to its size."

"I don't know Rodney," I admitted. "I just know the room I'm standing in is smaller than the one I saw on the map." I walked around slowly before coming to rest in front of the wall directly opposite the door. "This wall," I said. "It shouldn't be here." I put my hand against the wall and felt a tingle. Up close I noticed that the wall was etched with ancient symbols enclosed in circles of varying sizes. At my touch a faint blue light traversed the wall, illuminating the symbols.

"Wow," Sheppard said. "Can we break through it?"

"Oh that's your solution to everything isn't it Major!" Rodney said heatedly. "If you can't work it out quickly then just blow it up! Well for your information that won't work here. The room is stable but I wouldn't recommend setting off any charges so close to the outer walls, not unless you'd like to go for an unexpected swim. Anyway I can't tell how thick this wall is so we have no way of knowing how much C4 we'd need to make a hole big enough. So to answer your question - no we can't break through it!"

"All right Rodney, keep your shirt on," Sheppard winked at me. He did enjoy getting Rodney riled up and I was pretty sure he did it deliberately.

"It's a puzzle," I breathed. "An ancient puzzle we have to solve."

"I kind of worked that out for myself Sabina," Major Sheppard drawled. He turned away to start organising the room for a longer stay but I barely registered his presence. I'd brought all my ancient references as well as the palm pad and I sat down on the floor in front of the wall and began to translate.


	23. Another puzzle to solve

**Chapter 23: Another puzzle to solve.**

The words were all wrong. No matter how much time I spent staring at the symbols I couldn't make sense of them. I'd been working on the wall for a day and a half and was already frustrated. Individually the symbols were all translatable but when I put them together they were just gibberish. I checked my watch ... I only had another 20 minutes before Major Sheppard arrived to force me to give it up for the day. Turning back to my notes I started again on the first section of the wall.

"Any progress?" Major Sheppard's voice startled me out of my silent contemplation.

"No," I said, resting my back against the wall as I looked up at him from my sitting position.

"Looks like Greek to me," he joked, coming over and looking down at my notes. "Hey isn't that the word for 'light'?" he asked, pointing to one of the symbols.

I turned the page upside down and looked at it closely. He was right! "How did you know that?" I asked him suspiciously.

"Hey you can't live here and not pick up a few words of ancient," he excused his unexpected knowledge.

Looking back at my upside down notes I realised for the first time that many of the symbols meant something else when looked at that way. Feeling a sense of discovery and excitement I walked to the wall and found the symbol Major Sheppard had pointed out. It was enclosed in a small circle - could it really be that simple? I put my hand on the circle and tried to rotate it clockwise. There was a faint stones rubbing against stones sound and the circle moved.

"That's it Major," I said turning back excitedly to my notes.

"Well I aim to please," he joked. "Need any more help?"

"Yes," I said, pulling him over to the wall. "Help me rotate this circle."

After an hour we had rotated all the circles in such a way that the passage almost made sense.

"What does it say?" Sheppard asked as we started to push the last circle into position.

"The chosen shall bring forth the key to destroy the ancient enemy and return light and life back to the galaxy" I paused to read my translation. "Or something like that."

Before he could say anything else the last circle clicked into place and we heard an ominous rumbling sound. Pulling me away from the wall, Sheppard stepped back and shone the light from his P90 into the gap that was emerging. After the dust had cleared the light revealed a chamber with a strange looking device in the middle. It looked like a table with square stone blocks of various sizes and heights on top of it. Each had symbols on them and there were more symbols on the walls.

"Oh great," I said tiredly, "another puzzle to solve."

"Elizabeth," Major Sheppard said into his radio. "We found the weapon."

Up until now the ancient palm pad hadn't been of much help, even though ancient Elizabeth had said it would be. Once Rodney had seen the weapon though he began muttering about schematics and rushed back to his lab to consult his research. And I began the task of translating the new batch of ancient we'd discovered, knowing this was going to take much more than a couple of days.

Major Sheppard went off world to Dagan, one of the addresses ancient Elizabeth had given us. Obviously we would need a ZPM to power the shields and I had assumed that would also apply to the Wraith weapon.

Rodney had been right in his initial mutterings - the ancient palm pad did contain some schematics for the weapon and once they were translated from ancient he was able to speculate a bit on how the weapon worked. He believed it was capable of tuning into some kind of frequency and using that to target the Wraith somehow. We had discovered straight away that each block that made up the weapon could be pushed down and that this affected the positions of the other blocks - Rodney said this was how the frequency must be set. But without knowing what frequency we were looking for or how to get the machine to align with it we were almost back to square one. I was sure the answer was written somewhere on the walls of that room, hence my compulsion to translate everything as soon as possible.

I was still on edge whenever Sheppard's team was off world – even after all this time I hadn't gotten used to trusting that they'd be all right, that they had the skills to get themselves out of trouble. Although I spent most of my time down in that room I was still aware of the passage of time and began to worry when the Major didn't return when he should have.

I was never gladder of Sheppard's over protectiveness than when a lone Wraith dart flew over the city and scanned us. He had insisted that while he was gone, I could only go down to the weapons room if I took one of his men with me. Today it was Private Mason. The Private told me to get down and remain still as the dart flew directly over us, chased by three of our jumpers. I didn't see anything so far down in the city depths but I felt disorientated and there was a strange buzzing in my ears. I hadn't been blocking myself from the sensors because Dr Weir had asked me not to but right then I felt the need to be invisible again and re-established my block. Almost immediately I began to feel better, and turned my attention back to the weapon. I felt a huge relief when Mason informed me that the danger had passed.

"Interesting," I mused. The section of the wall I was looking at talked about the hands of the chosen together bringing alignment to the console. That sounded promising. I looked around, trying to find anything that would correlate with that. There was a border running all the way around the table and I noticed for the first time that one part of it seemed to have been added on after its initial construction.

I pulled out the pocket knife Major Sheppard had given me at the end of basic training and used it to pry up the top of that section, grabbing it when the gap was big enough and gently lifting it away. Beneath it were carved indentations in the shape of two human hands, fingers outstretched. Without thinking I placed my hands on each spot. A surge of ancient power shot out of the console and travelled up my arms. I felt like my very blood was on fire and that my head would explode from the mental pressure the machine seemed to apply. The sensation was more than I could bear and I tried to rip my hands away but they seemed to be fused to the table. Crying out in pain I saw Private Mason running into the room from the corridor where he'd been checking in.

"Get back," I yelled, still struggling with the device. My consciousness narrowed and the edges of my vision turned black. Snakes of energy were flashing out of the device now and one of them struck Private Mason, sending him flying across the floor. I could feel my body slip from the machine to the floor as I made a last desperate attempt to shut off the device in my head. Then the darkness took me.

Authors Note: Sorry about the spoilers for Stargate SG1 The Reckoning Part 2 - I didn't want to put a warning in before hand in case that gave away what the weapon was ... from my understanding the Ancients built the gate system and everything else Ancient that SG1 ever found in our galaxy BEFORE they went to the Pegasus galaxy. The weapon on Dakara was incredibily powerful AND capable of defeating a whole race - it doesn't seem out of character for them to make another weapon in the Pegasus galaxy once the threat of the Wraith got so out of control. They'd want to make it a bit more secure though - hence it being something under development rather than something they deployed (making their retreat back to our galaxy unnecessary - which clearly it was!) Well, that's what I think happened anyway!!


	24. You put your hands on them?

**Chapter 24: You **_**put**_** your hands on them?**

The next thing I knew I was waking up in Dr Beckett's infirmary to the site of Major Sheppard dosing in a chair beside my bed. Of course I'd been down to the infirmary lots of times before but I realised this was the first time I'd been an inmate. As I became more aware of my surroundings memory came back and I looked down at my hands. They were both covered in white bandages and I wondered how bad it was - I couldn't feel any pain but that was probably because Carson had dosed me up with some nice pain killers.

"Major," I croaked too softly for him to hear. Clearing my throat I tried again. "Major!"

"You're awake," he snapped to attention instantly. "How do you feel?"

"Stupid," I said bitterly, shifting restlessly in the bed. "How's Private Mason?"

"He'll be fine," Sheppard reassured me. "He'll need a few days to recover fully - Carson said he had every appearance of having been struck by lightning."

"I'm glad he's okay," I whispered, thinking back to what had happened. "Did you get the ZPM?" I asked before he could question me further.

"No," Sheppard replied with a frown. "We found it after having to dig up half the planet, solve a puzzle, _and_ outsmart the Genii. Rodney stupidly told the Dagan's we weren't the ancients and they refused to let us bring it back."

"Is there any chance they'll change their minds?" I asked.

"Nah, they said they're going to hide it again until the Ancients return and they get their reward."

We both fell silent for a moment, before Major Sheppard reached out and carefully touched one of my bandaged hands.

"So tell me what happened." his voice was firm and I knew I'd used up his patience and would have to admit to my own stupidity.

"There was a reference on the wall to the hands of the chosen," I said, trying to be brief. "I found a part of the console with spots to put my hands so I just ..." my voice trailed off.

"You _put_ your hands on them?" Sheppard's voice was incredulous. "What the hell were you thinking?"

"_I wasn't thinking_," I snapped back. "The city is starved for power - I didn't consider the fact that the weapon might have an independent power source. I tried to pull it back once I realised what was happening but it was really difficult to get control. I did manage to shut it down eventually but I didn't have enough left over to stop myself passing out."

"I left Private Mason down there so you couldn't go off and do something stupid but you _still_ managed to find a way to pull it off," Sheppard was clearly less than impressed.

"It wasn't that bad," I protested his over reaction to what seemed to be minor injuries.

"That puzzle on Dagan had spots to put your hands too," Sheppard informed me. "One of Koyla's men put his hands on it, touched the wrong buttons and it killed him!"

"I didn't _know_ that," I defended my actions.

"Enough crap has happened from people touching Ancient technology!" Sheppard pointed out. "You should have expected the worst! In fact let's make a new rule – no touching the Ancient stuff without McKay's approval."

"Ha, Ha," I said. "It was worth a couple of sore hands," I told him. "We needed to know how the weapon works and now we're much closer than we would have been. That Wraith dart came here for a reason - we may not have a lot of time to figure this thing out."

"You've got that right," Major Sheppard had a worried look in his eyes. "There are 3 hive ships heading our way – they'll be here within 2 weeks."

"_Crap_," I said weakly trying to sit up. "I need to get out of here and back to the weapon."

"Not until Carson says you're good to go," Major Sheppard pushed me back down far too easily.

"Okay, then go get him so I can get out of here,' I commanded briskly.

"Yes Ma'am!" Sheppard flipped me a mocking salute before turning to get Carson. When he got to the door he turned back with a serious look. "I'm glad you're okay," he said quietly before turning to find Dr Beckett.

Dr Beckett released me from the infirmary just before lunch time with a promise that I'd check in with him the next morning. I realised I hadn't eaten in some time so I headed to the commissary, not surprised to find it humming with muted conversation. I saw Teyla sitting with Dr McKay, and was relieved when she motioning for me to join them.

"It is good to see you are well," Teyla commented with a smile. "We were most worried when we discovered you unconscious on the floor of the weapons room."

"_We_ were worried," Dr McKay quipped, gesturing to himself and Teyla. "_Sheppard_ was freaked out."

"Rodney!" Teyla reprimanded him.

"What? Like she's not going to hear it from someone else?" Dr McKay protested before continuing. "I've never seen him look so pale - I thought he was going to faint and wouldn't that have been justice after the number of times he's hassled me since I passed out that one time?"

"Well, it wasn't my finest hour," I admitted, ignoring what Dr McKay was saying. I didn't believe for one minute that Major Sheppard had been weakened in any way by the prospect of me being injured.

"You are definitely on to something though," Rodney looked up from the sandwich he had been eating at a rapid pace. "I took some readings and I think we can rig something up to work out how much power we have. It's not a ZedPM because I would have detected that when we first got here but it could be something like the system that runs the Stargate. It's good to know the ancients didn't power everything in Atlantis with a ZedPM."

Before I could respond my eyes were drawn to the entrance where Major Sheppard had just appeared. It only took him a second to spot me in the crowd (how does he do that!) and he made his way over to us. It had been some time since I'd allowed myself to truly make eye contact with him - his sudden appearance had our eyes locked from across the room before I could look away. I felt heat suffuse my face and my heartbeat quicken as he stopped in front of me, still just looking at me.

"Hello?" Dr McKay's voice demanded attention. "Atlantis to Sheppard!" he added, interrupting our silent communication.

"Rodney," Sheppard said, still looking at me. "Elizabeth wants to see us all to discuss our options. You okay?" he questioned me.

"I'm fine," I said firmly. "Ready to get back to it." I added as Teyla and Rodney got up and left the table, nodding to me in farewell.

"I thought you'd say that," he acknowledged. "Private Spencer will be accompanying you - he has orders to make sure you don't touch anything else."

"I wasn't planning to!" I said indignantly. "At least not until I've translated the rest of the walls," I muttered under my breath.

"I need to get to this meeting," he frowned at me, clearly worrying about what I'd meant by that comment. "Stay out of trouble! I'll catch up with you later." He stroked a hand down my pony tail before turning and following Teyla and Rodney from the room.

I glanced around to see if anyone had noticed and gave a weak smile when I saw a few people looking my way with knowing looks. Looking back down at the food I hadn't yet touched I couldn't help but think about what Rodney had said. Had Major Sheppard really been that affected by my collapse? Could I possibly be any more confused and divided about him?

I was still puzzled by that connection we had that I knew _did_ have something to do with the ATA gene. I wasn't up to that level of thinking after my experience earlier in the day so I resolutely pushed it all to the back of my mind again. It was getting pretty crowded back there.


	25. Do you want to send a message home?

**Chapter 25: Do you want to send a message home?**

"I'm going off world with Teyla," Major Sheppard told me at breakfast the next morning. "Zelenka worked out where the hive ships will be stopping. We need intel and there's a planet close by where Teyla is well known."

"Oh," I tried not to let him see how much that worried me. "Be careful ... I know – you're _always_ careful!"

"I wasn't gonna say that," he denied with a smile. "I was gonna say _you_ be careful too."

"I'll do my best Major," I looked up at him with a smile of my own, a smile I couldn't hold as I watched him walk away.

I went down to the Wraith weapon room as soon as he was gone, intending to continue my work as best I could. It was difficult with my hands bandaged to work quickly but Dr Beckett had assured me there was no serious damage and that the bandages would be off in a couple of days.

As usual, Major Sheppard didn't return when he was scheduled ... I spent every waking hour in the weapon room, frustrating myself with my lack of real progress. I'd translated many sections on the walls but none of it had anything to do with how the weapon actually worked. I was beginning to worry that the weapon would be like every other piece of Ancient technology we had found - long on potential, short on instructions!

It was almost two days before Major Sheppard finally returned. "How's it coming? he asked by way of greeting.

"Slow," I admitted, relieved that he was home safe. "Why don't you have another look, Mensa Boy?"

"Rodney _told_ you about that?" Sheppard looked uncomfortable.

"Only to complain that you refused to join his Atlantis chapter," I laughed at his expression of distaste at the thought. "Who knew you were a geek?" I teased.

"Don't laugh too hard," he took delight in informing me. "I saw your test results – apparently you could be a Mensa geek too if you wanted."

"No way," I denied.

"_Way_," Sheppard insisted.

"Well, don't tell Rodney," I said dismissively. "I don't want to join his Atlantis chapter either." I turned back to the wall, trying to continue my work but too aware of Sheppard standing silently behind me.

"How was the mission?" I asked casually.

"Don't ask," he replied. "We got the intel we needed and we saved a few people from the culling. One of them is a friend of Teyla's."

I knew he was leaving out much of the detail but I also knew that pressing him now would only make him defensive. Even though I'd never seen a Wraith myself I was filled with anger at their callous disregard for human life in this galaxy.

"Do you want to send a message home?" he abruptly changed the subject.

"What?"

"McKay found a way to send all our Intel to Earth through the Stargate. Apparently even though we only have 1.3 seconds to get the message through there's still a _whole_ second left. Dr Weir suggested we could all send video messages to our families. Do you want to?"

"I'm good," I refused, looking back at my notes.

"You don't want to tell your family you're okay?" Major Sheppard asked in surprise.

"No family," I rushed that one out.

"Well, what about friends then?" he persisted in digging at me.

"No friends," I said it even quicker, trying to give him the impression that I was completely fine with that.

"Surely there's someone back on Earth who'd be happy to hear you're okay?" he said in disbelief.

"No one that would miss me if I disappeared," I admitted. "Can you just drop it please, because I really don't want to talk about it."

"I don't have any family either – parents died in a car crash a few years back and I never had any siblings," he said it quietly.

"That's sad," I said softly. Of course I wanted to know more about the Major but at the same time I was unwilling to enter into a deep and meaningful conversation if it meant I had to reciprocate.

"I tried the whole marriage thing but it didn't last very long," Major Sheppard continued. "Long absences and too many secrets killed things before they really even got off the ground. Moving around with the air force, especially my last posting at McMurdo, doesn't make for keeping non military friends."

"Why are you telling me this?" I looked over at him before looking away again.

"I realised when Elizabeth mentioned letters home that I don't know anything about your life before you came to Atlantis," Sheppard admitted, moving to stand just a short distance away from me. "I thought it might make you feel more comfortable telling me about you if I shared a little of my past."

"Well it doesn't," I retorted, turning my back to him. "You want to know? _Fine_. I never knew my parents, grew up in foster care moving from family to family because I was never good enough to be adopted. As soon as I was old enough I went out on my own. I couldn't work out what I wanted to do with my life though so I just drifted from place to place doing whatever jobs I could get. Never stayed anywhere long enough to make friends. End of story."

"I'm sorry," Major Sheppard said quietly, putting his hands on my shoulders and squeezing gently. I tried to shrug him off but as usual found that he could be pretty persistent when he wanted something.

"I'm sorry you never found your place back on Earth, never found people who could appreciate you." I snorted in disbelief at that last bit. Major Sheppard turned me around so he could see my expression. "You have a place here," he said it with firm resolve, "and I'll do whatever it takes to make sure it's never taken away from you."

My eyes began to water as I registered the commitment he was making to look after me. Leaning my head against his chest I whispered a grateful thank you. I felt him kiss the top of my head as he held me, circling a hand over my back as he patiently waited for me to get myself back together.

"Happy now?" I finally asked, pulling away from him and swiping an embarrassed hand across the tears still on my face.

"Not quite," Sheppard drawled. "But I'm getting there."

"Good for you," I quipped, trying to put some emotional distance between us. "I need to get back to this so if there's nothing else ..."

"I'm going," he said.

I went back to my work with a lighter heart, and a smile on my face.

Authors Note: Sorry for the slight fluff element ... I think the lack of emotional ties is a crucial element in what motivates people in times of crisis. Anyway, on with the next chapter!


	26. You have Wraith DNA

**Chapter 26: You have Wraith DNA.**

I spent pretty much all my time in the Wraith weapons room after that, including sneaking back during the night when everyone believed I was sleeping. I had finished translating all the symbols and felt I should fill Dr Weir, Dr McKay and Major Sheppard in on what I'd learnt. I have to say it was a little daunting to be in the briefing room for the first time and have everyone's eyes on me, waiting for me to speak.

"Dr McKay was right," I smiled at his smug grin. "The weapon is based on finding a specific frequency for the Wraith. Unfortunately it doesn't say how to find that frequency ... the only reason I can think of for that is that it was something so obvious they didn't feel the need to write it down."

"As we've already seen, the ancients weren't that good at writing down instructions for any of their technology – we're lucky there are schematics at all, even if they're woefully incomplete." Rodney said scathingly.

"I've hooked up a laptop to the device," Rodney continued. "Dr Beckett thinks he can use the Wraith samples he got from our captive in combination with the machine – it would mean a process of trial and error to alter the position of each block on the device until it seems like we have a match." Rodney shook his head as he admitted "there are millions of combinations of positions for those blocks and what's worse you change one position which gets you closer but then when you change another it messes up what you had and you end up further away. It's not looking good."

"So we can't use the weapon?" Dr Weir asked.

"Not exactly," I disagreed, deliberately not looking anywhere near Major Sheppard. I knew he was not going to like the next bit. "The device was meant to be operated by _'the chosen',_" I emphasised that title. "From what ancient Elizabeth said it's safe to assume that I qualify for that position. I think it's worth the risk for me to reconnect with the machine like I did before and attempt to get it running."

"No way," Major Sheppard's protest was immediate. "That machine almost killed you the first time and you want to go sticking your hands on it again?"

"I wasn't prepared last time! Besides, I don't think it's up to you Major," I stated, looking to Elizabeth for support. "Three hive ships will be here in less than a week – the time for caution is over! We need every advantage we can get and the ancients meant that weapon to be the final defence of Atlantis!"

"I don't care," Major Sheppard said hotly. "You're not doing it!"

"Don't tell me what I can and can't do," I almost yelled.

"Sabina! Major! Please!" Dr Weir broke in. "While I appreciate your willingness to try this Sabina, for the moment I agree with Major Sheppard. We have no way of knowing what that machine is capable of and until I see something concrete to show me we won't end up blowing ourselves up instead of the Wraith I don't think we can risk it. Yes we're running out of time, and yes we may want to revise that if things get a lot more desperate, but we're not there yet. For the time being I suggest you keep studying the device _without_ touching it. If you can show me that you know exactly how it's going to work then, and only then, will I reconsider."

"Okay," I said to Dr Weir reluctantly. "I'll keep studying, and try to understand more about the device."

The meeting was clearly over so I jumped up to get out the door as quickly as possible

"Sabina," Major Sheppard's voice stopped me in my tracks. "A word please."

"I'll give you a word," I said in a low tone, waiting for the others to leave. "How about _arrogant_ arse!"

"That's two words," he pointed out. "Here's a word for you though – _reckless_!"

"I'm not reckless," I denied his accusation. "But I can't sit around enjoying your protection when I _know_ there's something I can do to help."

"I'm not saying you should, just that you shouldn't be so quick to rush in before you know the full situation." Major Sheppard insisted. "I ... Yes Carson?" he was interrupted by the Doctor on his radio.

"I need to see you immediately," Dr Beckett said, "and Sabina as well."

"Okay Doc," Sheppard agreed. "We'll be right there."

With a sick feeling of dread I had the sudden realisation that things were about to get much worse.

"Major, Sabina," Dr Beckett greeted us. "Thanks for coming down." His whole demeanour came off as somewhat nervous, a view Major Sheppard seemed to share.

"What's wrong Carson," he asked.

"Well, as you know, we found out yesterday that Teyla has some Wraith DNA," he began.

I looked at Major Sheppard with a raised eyebrow. "I was gonna tell you," he insisted.

"It was easy to miss – not surprising given I had no way of making the necessary comparison between Teyla's DNA and Wraith DNA." Dr Beckett continued. "It was the information you brought back from that planet that made it possible to identify."

"I _know_ all this Carson," Sheppard protested. "Get to the point."

"Okay," Dr Beckett said reluctantly. "It struck me this morning that there was something familiar about the strands I've isolated as being Wraith. I've seen them before," Carson looked at me uncertainly, "in your DNA Sabina."

"How's that even possible?" Major Sheppard reacted. "Sabina's not from the Pegasus galaxy – she's never even _seen_ a Wraith!"

"I can't explain it Major," Dr Beckett said. "But there is no doubt. There are a few differences but the match is close enough it can only be Wraith DNA. Sabina has additional rogue DNA I still haven't identified but some of hers is definitely Wraith."

"I think I can explain it," I said in a small voice. "It's here somewhere in my notes," I thumbed through the pages I still had with me from the meeting with Dr Weir. "I worked out pretty quickly that the machine was keyed to a specific subset of the ancients, much like the rest of their technology except not only was the ATA gene required but something additional as well."

I looked down at my notes and read "The chosen gave themselves up as tainted to make the necessary connection for the final protection of Atlantis". I stopped reading and looked up to judge their reaction. "I thought it meant that it was some naturally occurring degradation in DNA they took advantage of in designing the weapon but it wasn't that at all. Some of them willingly submitted themselves to be genetically altered – obviously with Wraith DNA. They never got the chance to activate the weapon and the few remaining chosen retreated through the gate to Earth with the rest of the population. They passed on those Wraith genes much the same as the ATA gene has been passed on."

"Aye, that makes sense," Dr Beckett agreed.

"Teyla can sense the Wraith," Major Sheppard commented. "If Sabina has Wraith DNA too, how come she can't do that?"

"I've never been anywhere near a Wraith," I reminded him. "Maybe I could sense them if I were close enough and I knew what I was looking for."

"What about that day the dart flew over Atlantis – did you sense anything then?" Sheppard persisted.

"I was a long way from its flight path," I pointed out, trying to think back to that day. "I recall feeling a little dizzy and hearing a buzzing in my ears, but it quickly passed once I re-established my sensor block."

"Well," Dr Beckett commented. "From the sounds of that it seems that maybe you could sense the Wraith if you were close enough and you weren't shielding yourself."

That made sense – the mental blanket I placed over myself was a barrier between me and detection. Clearly that could work both ways, making it hard for me to detect anything as well.

"I don't think you should start experimenting trying to sense the Wraith," Major Sheppard cautioned me. "Teyla's been doing this since she was a child."

"I wasn't going to," I denied distractedly. Thoughts were zooming through my brain as I realised the implication. I had Wraith DNA which meant I had it within myself to tune in the Wraith frequency for the weapon. I was sure the hand controls were the way in which the individual blocks should be set. I just had to work out how I was going to control the device for long enough to put the frequency into place.

I found out later that day that Teyla had managed to connect with a Wraith and learnt that they were coming here as the only means of making it to Earth and a new rich feeding ground. Time was running out.


	27. It will be Major Sheppard's decision

**Chapter 27: In the end it **_**will**_** be Major Sheppard's decision.**

Things started to move very fast after that. Dr McKay headed out to the LaGrange satellite weapons platform – our main hope for defeating the three hive ships before they even got to Atlantis.

Major Sheppard took the rest of his team out to look for a new alpha site for the evacuation. I didn't want to leave Atlantis and hoped that it wouldn't come to that. It saddened me too that our backup plan was to destroy Atlantis to prevent the Wraith from getting their hands on it.

While Sheppard was off world I gathered together my notes and research with the plan of showing Dr Weir that using the weapon was a viable option, should the satellite prove ineffective.

"Sorry to interrupt," I apologised as I walked in to Dr Weir's office. "Do you have a minute?"

"What can I do for you Sabina?" Dr Weir asked.

"I wanted to talk to you some more about the Wraith weapon," I said. "I've done all I can to work out a plan for using it and I think it's viable."

"Okay," Dr Weir said. "What's your plan?"

"Well," I began. "The ancients deliberately altered themselves with Wraith DNA and it seems pretty clear from the writings in the weapon room that it was an essential part of the weapons design – obviously so they could tune the weapon specifically to the Wraith alone. The references to the 'hands of the chosen' make it clear that the hand pads were the way the ancient operator was supposed to key in the frequency. If it was as simple as just putting in a frequency then the ancients could have just pre-programmed it. I think that the Wraith DNA was needed so the operator could do what Teyla has been doing – actually connect to a Wraith ship. The machine would then connect to that Wraith presence, take the frequency needed, and set off the weapon." I paused to take a breath, surprised that Dr Weir hadn't interrupted me so far.

"The weapon creates an energy vortex ... when the power has built up enough it shoots out an energy beam to encompass the whole city that will destroy every living thing it passes through," I said. "The key factor is the frequency – it only destroys living things corresponding to that frequency. The range of the weapon is limited too – it'll take out any Wraith in the city as well as any in orbit but nothing beyond that. The ancients were still working on a way to take the effect throughout the whole galaxy. The weapon was being constructed at the height of the siege against Atlantis - their resources were divided to such a point that they were forced to abandon the city before they solved the problem."

"Did you determine how the weapon is actually operated?" Dr Weir asked.

"The ancient gene is required so there's a mental effort necessary to control the weapon," I said. "The Wraith gene is required to connect to nearby Wraith to get the frequency so that's about mental control too."

"So you believe with sufficient mental control of both your ancient and Wraith genes, you'll be able to operate the weapon successfully?" Dr Weir confirmed her understanding of what I was proposing.

"Yes," I confirmed. "Teyla has made progress on connecting to the Wraith – she could teach me how to do that. As for the ancient gene ... I've been practising for hours every day and I believe I've attained the level of control necessary to make sure the power doesn't overload like last time."

"Didn't Rodney say that the possible results of activating the weapon were too unpredictable to make the risk worthwhile?" Dr Weir questioned.

"From what's written on the walls in that room, the Ancients meant the weapon to be used to defend the city - they wouldn't have done that if the weapon was dangerous to Atlantis. I _can_ do this Dr Weir," I stated firmly. "I'm willing to put in the effort necessary to make sure I can control the outcome."

"Okay," Dr Weir acknowledged that statement, clearly thinking over her options before coming to a decision. "Work with Teyla on finding a safe way to connect to the Wraith. _If_ that goes well, and _if_ the Wraith get close enough to the city to make the weapon useful, then we'll decide if we're ready to pursue using it."

"Thank you Dr Weir," I said with relief.

"Don't thank me yet Sabina," Dr Weir cautioned. ""If the Wraith get that close to the city the military will be fully in charge – in the end it _will_ be Major Sheppard's decision as to whether we actually deploy the weapon. I suggest you work out how you're going to convince him you're ready to do this."

Authors Note: Timing wise, from what I can work out, Season One of Atlantis and Season 8 of SG1 are sort of happening at the same time - hence Dakara hadn't happened and being cut off from Earth when it does happen Atlantis wouldn't know about it (and so wouldn't know to use the Stargates to spread the effect of the weapon). I also think the Ancients in redesiging the weapon would have thought to make it much harder for it to be used for anything other than it's intended purpose.

Thanks to everyone reading my story - hope you're still enjoying it.


	28. Shouldn’t we be able to connect?

**Chapter 28: Shouldn't we be able to connect to each other?**

I spent the rest of that day thinking over how to approach Major Sheppard. I knew it wouldn't be easy and I didn't have a clear plan but when I heard that Sheppard was back from the latest alpha site mission I decided to tackle the problem straight away. Using the sensors I asked Atlantis to tell me where Major Sheppard was and determined he was in the commissary – it _was_ dinner time so maybe I could have just worked that one out by myself.

Finding a specific person using the sensors was another new skill I'd acquired recently. Unfortunately it required me to know how a person 'felt' to Atlantis so it was only useful for people with the gene that I'd previously done some kind of exercise with the sensors on. That meant only the Major and Dr Beckett at this stage.

"Is this seat taken?" I asked Major Sheppard – he was sitting alone reading a report while he ate his dinner.

"I already spoke to Weir and the answer is no," Sheppard replied without even looking up at me.

"How can you say that?" I asked in a frustrated voice, sitting down in the chair opposite him. "At least give me the chance to explain what I've learned!"

"Won't matter," Sheppard said, finally looking at me. "It's too dangerous. You're not doing it."

"You are the most annoying ... arrogant ... _annoying_ ... man!" I almost growled. "I bet if it was a machine that _you_ could operate you'd be all over it no matter what the danger was!"

"Maybe," he conceded, pinning me with an intense look. "But it'd be my job to do that to protect all the people under my charge and under my command. It's your job to help the science department with ancient translations and technologies – _not_ to recklessly risk your life on something with such an uncertain outcome. Besides, McKay is on his way to that weapons satellite right now. That thing is supposed to be capable of wiping out all three hive ships so we might not even _need_ the Wraith weapon."

"How likely is it that Rodney will get that satellite fully operational?" I allowed myself to be momentarily sidetracked.

"Okay, it's a bit of a long shot," Sheppard admitted. "It's been out there for 10,000 years and McKay wasn't sure that power was even the problem. Dr Weir has the evacuation and self destruct plan as our fall back."

"So you'd rather see Atlantis destroyed that let me do what I know I _can_ do?" I asked in disbelief.

"You haven't shown me anything to convince me using that weapon is even possible," Major Sheppard protested. "I'm not willing to jeopardise _anyone's_ safety on what frankly looks like an extreme long shot at best!"

"Dr Weir is allowing me to work with Teyla," I said. "If I can prove that I can control a connection with the Wraith to her satisfaction, will you reconsider?"

"Dr Weir told me she was letting you do that," Major Sheppard leant forward, resting his hands close to my own but not touching me. "And I told her that I didn't agree with that decision and that it wouldn't impact on the decision I'd already made not to make use of the Wraith weapon."

"What if it was someone else?" I asked, changing tact. "What if we found someone else who had the ATA gene and the Wraith gene? Would you let them do it?"

Major Sheppard looked away as I asked that question, rubbing a hand over his forehead as though I were giving him a headache. I could almost see him trying to come up with a logical way around that one. "If they were in the military then maybe, and I do mean _maybe_, I might be willing to let them have a go if the situation were dire enough," he admitted.

"Okay, then I'll enlist," I threw out that challenge.

"No you won't!" Major Sheppard protested. "There is no situation I can think of where I'd willingly agree for you to be under my command again."

"Why the hell not?" I argued heatedly. "If I enlisted then it _would_ be my job to take whatever steps were necessary to protect Atlantis!"

"You _know_ why not," Major Sheppard's voice was full of all the things still left unspoken between us. "Besides, I don't have the power to accept enlisting personnel here – you'd have to go back to Earth for that and we know that's not possible so forget about it."

"But," I began, trying to keep the discussion open.

"That's enough!" Major Sheppard interrupted. "It's been a long day and I still haven't found a suitable planet for the alpha site. I'm not in the mood to argue with you."

"_Fine_!" I almost shouted as I jumped up from the table. "I can see my petty little problems aren't of interest to you right now so I'll go and take them somewhere else."

"Sabina," I heard Sheppard call out as I made a hasty retreat. I didn't look back.

It was so frustrating to believe so completely what your role was meant to be and have no one else support that. I was sure that I could do what was required in spite of what Major Sheppard thought. I had permission from Dr Weir to proceed up to a certain point – I didn't need the Major's permission for that. And so I decided to ignore what Sheppard had said and do everything I needed to do so that if it came down to it, I would be ready to use the weapon.

Teyla was somewhat reluctant to assist me with making a connection to the Wraith, despite having told Dr Weir she would do what she could.

"It is dangerous and draining," she informed me when I asked her later that evening if we could begin. "I am not sure it is wise to attempt this type of connection when the need is not crucial. The Wraith could take control of you instead and gain valuable information to use against Atlantis."

That was a valid point – I didn't want to do anything to risk alerting the Wraith to the presence of possibly the only weapon capable of destroying them en masse.

"Could you train me yourself?" I asked, having a different idea.

"I am not sure what you mean," Teyla admitted with a puzzled frown.

"You have the Wraith gene," I pointed out, "and so do I. Shouldn't we be able to connect to each other?"

"I had not thought of that," Teyla was intrigued by the idea. "I believe you are correct – a connection such as the Wraith use should be possible between us."

"Okay," I said with a smile. "Progress! Let's go talk to Dr Beckett so we can get started."

"It is late and Dr Beckett informed me that you have not been sleeping well," Teyla said firmly. "I suggest we both get a good night's rest and begin in the morning."

"I'm fine," I protested. "The Wraith could be here any time – we need to hurry before it's too late."

"Connecting with the Wraith requires strong mental concentration," Teyla stated, "the type that can only be achieved after sufficient rest."

I knew how futile it would be to argue with her – Teyla was very determined and seldom gave way when she had set her mind on a course of action.

"Okay," I reluctantly agreed. "Thank you for agreeing to help."

"I will meet you in the infirmary at 8 am," Teyla took her leave with a serene smile in my direction.

I thought about going back to the weapons room to check out a few things but decided that perhaps Teyla was right and I did need the rest. The fact that I spotted Major Sheppard heading towards me from the direction I would have had to take to get there had nothing to do with it. Honest.


	29. What ever happened to 'Stay Positive?

**Chapter 29: What ever happened to 'Stay Positive'?**

The next morning I awoke feeling much better than I had in a while. Thank you Teyla! After a quick breakfast on the run I rushed down to the infirmary to talk to Dr Beckett. Teyla had not arrived yet - I noticed Sergeant Bates in one of the beds and looked over at Dr Beckett with a raised eyebrow.

"He was beaten pretty badly," Dr Beckett admitted. "There's some suspicion that Teyla might have had something to do with it."

"Teyla would never do that!" I denied the possibility.

"I know lass," Dr Beckett agreed. "We're waiting on some test results – I should know more by the end of the day."

Teyla rushed in at that point, apologising for being late. Sheppard and Ford had met with her in her quarters about Sergeant Bates and had delayed her in the process.

"John wouldn't believe you had anything to do with this," I assured her.

"I hope not," Teyla acknowledged before adding "Shall we begin?"

"Can you hook us up so you can break the connection if this actually works and we get into trouble?" I asked Carson.

"Aye," Dr Beckett agreed readily. He got us set up on two adjacent beds and hooked up the sensors.

"Are you ready?" I asked Teyla. We had agreed that I would attempt to make a connection to her using the method she had described to me. If I made a connection Teyla would then attempt to reverse it and get into my mind instead. My job would be to resist that.

"Proceed Sabina," Teyla said softly, relaxing against her pillow. "I am ready."

It was the strangest feeling to send my mind out and into someone else's head. Teyla's instructions were effective and I made the initial connection with ease. I had thought the sensation would be similar to what I felt when I used ancient technology and although it was, my experience there didn't help me. Apart from getting the sense of how controlled and ordered her mind was, that first connection was so brief it was over before it began. I felt Teyla invade my mind almost immediately and tried to put up a block so that she couldn't take control. At first I could block her but the mental effort required was extreme and I began to tire. Before my block could crumble completely, Teyla released me and I opened my eyes to see Dr Beckett looking at me curiously.

"Did it work?" he asked, almost excited.

"It did," Teyla said. "Sabina was able to make the connection with ease; however she must develop more mental strength if she is to stop a Wraith from taking control."

"What Teyla means is that I was barely able to hold the connection for a second before she took over," I admitted with a self deprecating laugh. "How effective was the block I put up?" I asked curiously.

"Although it was complete to start with," Teyla shifted to look at me closely, "it became less so as you tired. I was able to gain some access to your thoughts."

"Oh," I said. "Anything interesting in there?" I tried to lighten the suddenly tense mood descending on the infirmary.

"You need not worry Sabina," Teyla reassured me. "I will not divulge anything I might learn during our practice."

Okay, that just made me more worried. What was I unwittingly giving away by making myself vulnerable to her and did I want Teyla to know that much about me?

"Shall we try again?" Teyla broke into my thoughts.

"Huh? Oh right, yes – lets." I replied, worrying about the things I didn't want _anyone_ to know while at the same time trying not to worry about them. My head was already beginning to hurt.

We practised for hours that day and by the end of it I had a massive headache but also a sense of achievement. By our last attempt I was able to hold my block indefinitely and Teyla agreed that with further practice I would be able to stop her from taking over the connection. Dr Beckett said that my many hours controlling the ancient technology would have strengthened my mind and that I just had to learn new ways to resist mental attack – something I wasn't used to because ... well Atlantis _liked_ me and would never attack me!

Unfortunately my practice with Teyla was cut short. Dr Beckett had proven her innocence in the attack on Sergeant Bates – by proving there was a Wraith in the city! Teyla rushed out immediately to assist in its capture.

Although the idea of practicing on a real Wraith was momentarily attractive I knew we couldn't risk giving anything away and we had no idea how much the Wraith had communicated to its ship. The fact that a Wraith had been in the city for two weeks freaked me out ... knowing that Teyla and Major Sheppard were out there hunting it down scared me even more. I was tired and had to make a more conscious effort to keep my sensor blocks in place.

Waiting it out in my quarters, I paced back and forth as I anxiously prayed that no one would get hurt. It was Dr Beckett who let me know that the Wraith had been apprehended - Major Sheppard had been stunned with the Wraith weapon and was recovering in the infirmary. I stopped in briefly and was relieved to see John sleeping peacefully – good enough for me to retire back to my room to sleep as well. I had a feeling it might be a while before we'd get the chance for a full night's sleep again.

Early the next morning I headed straight for the infirmary only to find that Major Sheppard had already left to interrogate the Wraith prisoner. I was still there when we heard the news that Rodney's team had got the satellite up and running just in time to confront the hive ships. I cheered with the infirmary staff as it was broadcast that one of the hive ships had been destroyed. And I despaired at the news that the satellite had been destroyed with no further kills, carrying away Peter Grodin in its destruction.

The mood on Atlantis was bleak as we all came to the realisation that we were out of options, a point that was slammed home when we all heard Dr Weir's city wide announcement.

"May I have your attention, please? This is Doctor Weir. Our plan to stop the Wraith armada has failed. They will make it to Atlantis. Therefore we must begin our evacuation plans. I wish I could tell you all that this is a fight that we will win, but I can't do that. I wish I could tell you that we will find a safe harbour when we leave here. I can't promise you that either. I can tell you this: up to now, you all have accomplished extraordinary things, and I believe that even in the face of an uncertain future, as long as we stay together we have a chance to continue to do so. Now, we all have our evacuation duties, so thank you -- and I'll see you on the other side."

So that was it ... I wouldn't get the chance to even try to use the Wraith weapon because we would have evacuated long before the hive ships were within range. I was upset that we'd be responsible for the destruction of a city that had stood firm for 10,000 years but deep inside a small part of me was relieved that the decision was out of my hands, that I was no longer under pressure to operate a weapon even the ancients had hesitated to use.

I had plenty to do before the evacuation but I decided food should be the first priority, especially as I was kind of hoping I'd run into Major Sheppard or Teyla in the commissary. My mood lifted when I spotted both of them at their usual table. The rest of Atlantis was already buzzing with activity only a couple of hours after Weir's announcement so I wasn't surprised to see the room was otherwise deserted. It would take the rest of the day and some of the night before the evacuation would be complete.

"Are you okay?" I asked, not directing my question specifically at either one of them as I sat down across from Sheppard.

"We are all fine," Teyla reassured me.

"And the Wraith?" I asked hesitantly. I could sense that something wasn't right but was it really my place to question them?

"Dead," Sheppard said in such a way that I knew he had been the one to kill it and that I would be getting nothing more of the story from him.

"I will leave you now," Teyla said unexpectedly, rising from her chair. "The mornings events have been ... unsettling. I am sorry we did not get the chance to practice more Sabina but I have much to do before the time to evacuate is upon us," she added before leaving the Major and me alone.

"Is everything really okay?" I asked softly. "I mean apart from the fact that the Wraith are coming and the 10,000 year old piece of technology we were relying on is out of the equation?"

"What ever happened to 'Stay Positive'?" Major Sheppard looked at me with a slight smile, already appearing to put the events of the morning behind him.

"It's been a long week," I excused myself. "Do you want to hear about my progress?"

"Not particularly," Sheppard admitted. "Teyla filled me in on the basics anyway," he added.

"Oh ... right ... of course." I said, realising we were now alone in the commissary. "I should probably start packing myself," I added, making no attempt to move.

"How's the headache?" Sheppard looked at me closely.

"How did you know I had a headache?" I asked incredulously. I'd had one since yesterday's practice with Teyla but I thought I was better at hiding things than that.

"Your eyes," he admitted. "The brown kinda goes greenish when you get angry, or upset ... or when you've been doing too much of the mental control stuff."

"That's very observant of you Major," I said stiffly, not sure how I felt about that. A silence fell over us as neither of us made any attempt to leave. It was kind of nice just sitting there quietly, enjoying his presence in a way I hadn't done since the whole Chaya incident.

"Sabina," he broke the silence to ask softly. "Do you think you could do one thing for me?"

"What?" I asked just as quietly.

"Call me John."

"Okay," I agreed easily. "But that doesn't mean I've given up on getting you to let me use the Wraith weapon."

"I never for a second thought it did," he drawled. "Walk me to my room?" he stood and held out a hand to me.

"Okay," I took his hand and let him pull me up from my seat.

John kept a hold of my hand after we were both standing and I didn't protest. We walked the busy halls of Atlantis hand in hand, neither one of us compelled to speak. A strange mood had descended upon us – I felt very keenly that old bond between us but for once it didn't frighten me. The Wraith were coming and it seemed wrong that the petty things that had kept us apart should remain a barrier between us.

When we arrived at John's door, he turned and looked at me intently. I gazed back at him, trying to convey my acceptance of the question I knew he was asking. Coming to an agreement without speaking, he opened his door and we both walked inside.

It was so familiar to be in his arms again, but at the same time so different. We had both changed ... grown, especially me ... in our time apart and that was reflected in how we came together. We had an unspoken agreement that we wouldn't talk of our feelings or any of the things that had held us back. In fact we hardly spoke at all.

The same heated urgency and need overtook us as it had in the past, even more so because I think at the back of both our minds was the thought that this might be the last time we would have the chance to do this. I let down my guard more than I ever had and as a consequence felt that deep connection, that electric jolt, I'd always felt with him down to my very soul. Emotion and passion enveloped us - it was over in an instant that was an eternity.

After, as I lay cradled in John's strong arms, I promised myself that soon I would work out what this thing was between us. But for now I would just enjoy it, enjoy that feeling of being safe. I knew the future was uncertain but that just made me gladder that I'd had one more chance to be with John.

Authors Note: I know - MORE fluff! I just can't resist ... but surely in reality if you really thought things were that dire you'd take the opportunity to connect with the people close to you ... also apologies for the bit in the middle where I just kind of reiterate what we all know happens at the end of The Seige Part 1 - I needed to put the series of events in my story and didn't want to do a big conversation between Sabina and anyone else. Only a few more chapters to go now!


	30. You are relieved!

**Chapter 30: You are relieved.**

John only allowed himself an hours rest before he insisted on going back to the control room. Kissing me in farewell he reminded me that I should pack my things up as quickly as possible and get to my designated evacuation group.

I had offered to pack up his stuff and did so quickly before returning to my room to do the same. When the evacuation plans were being drawn up I had managed to justify my need to be in the last evacuation group – although to be honest I think Dr Weir saw through my arguments to the fact that I didn't want to leave unless John was leaving too. There was no point in doing anything more with the Wraith weapon so I made myself useful packing the equipment for safe transport.

The time passed quickly and before I knew it I was being instructed to make my way to the gate room. I stood with my group, looking up at the control room. John was up there and it reminded me of that first day when I'd arrived and first laid eyes on him. Who would have thought that it would end like this?

The Stargate began its dialling sequence but before it could complete an incoming wormhole took over. The marines herded us to one side as the shield was lowered and four marines stepped through. I watched as John ran down the steps with Dr Weir and Lt Ford to meet them. More marines were coming through the gate, some wheeling large boxes of equipment. I edged a little closer so I could hear what was being said.

"Colonel Dillon Everett, United States Marine Corps," the leader crisply stated.

"You should know ..." Dr Weir began.

"General O'Neill sends his compliments on a job well done under extraordinary circumstances," Everett interrupted her to state. He saluted her before continuing. "You are relieved."

"Sir, we're about to evacuate," John informed him.

"Without a fight!" Everett stated in disbelief.

"Yes, sir!" John confirmed.

"On _my_ order," Dr Weir pointed out.

"That evacuation order is rescinded," Everett stated. He looked around the Gateroom before asking "I assume you've armed the self destruct device?"

"Sir, what happened, as Doctor Weir was trying to tell you ..." John tried again to explain the situation to Colonel Everett but he really didn't seem to be interested in hearing anything but the sound of his own voice.

"I am gonna need you to disarm it immediately," he interrupted again.

"Hold on a second, Colonel -- I don't think you fully grasp our situation here," Dr Weir had her own go at getting the Colonel to listen to them.

"You have three Wraith hive ships bearing down on your position and precious little to defend yourselves with," Everett stated with no emotion. "That about sum it up?"

"You got our message!" Dr McKay spoke up for the first time since the marines had arrived.

"We got your message," Everett confirmed.

"It's down to two hive ships. We managed to destroy one of them," Dr Weir reported.

"Good for you!" Everett congratulated Dr Weir condescendingly. "That should make my job a little easier." He started to head up the steps to the control room but no one else moved.

"What exactly is your job, sir?" John asked.

"I should think that would be obvious to you by now, Major," Everett said. "We are going to defend Atlantis at all costs."

The marines were moving us away from the gate room so I didn't get to hear the rest of the conversation. I couldn't believe it – Stargate Command had sent through reinforcements! Atlantis would get another chance for survival and the Wraith weapon was now back on the table. I would need another chance to prove that the it should be deployed in the defence of the city. I had no intention of approaching the arrogant Colonel Everett myself but perhaps Dr Weir could be convinced to raise it as an option. John wouldn't be happy but since he was no longer the ranking officer the final decision was no longer his.

John found me in my quarters late that night. I hugged him tight before pulling away to get a better look at him. I could tell that the hour or so he'd spent with the new leader of Atlantis had not gone how he would have liked.

"Can you stay?" I asked him up front, already suspecting what the answer would be.

"No," he admitted, smoothing his hand down my pony tail absently. "Too much to do ... and I'm not gonna put you in a position for criticism from someone who clearly has no interest in hearing about the way things are here."

"He was a bit arrogant, wasn't he?" I commented as John went to stand looking out at the ocean surrounding Atlantis.

"He doesn't like me," John said it like a statement of fact. I knew he had enough experience with the prejudiced opinions of commanding officers after his 'black mark' in Afghanistan to know he wasn't just imagining it.

"He doesn't _know_ you," I pointed out – all that really needed to be said under those circumstances. "Can they defend Atlantis?"

"If the Colonel actually listens to people like Dr McKay then maybe," John replied, turning away from the window to look back at me. "But it won't be easy. A ZPM to power the shields is on its way on the Daedalus but it won't get here for 4 days – we have to hold Atlantis until then."

"With _what_?" I asked incredulously.

"Six naqahdah enhanced nuclear warheads, twelve hundred megatons apiece," John replied with a faint smile. "Apparently they emit almost zero EM and are otherwise invisible to radar. The plan is to deploy them in space and then detonate them by proximity fuse. They've also got some rail guns for close in fighting."

"I'm not sure what all that means," I admitted, "but it sounds pretty good!"

"They've brought a new naqahdah generator for the command chair too" John added. "McKay will need to hook it up and test it tomorrow – can you help with that?"

"Okay," I agreed. "What will you be doing?"

"Teaching marines how to fly the jumpers ... planting nuclear warheads in space ... you know, the usual." John tried to lighten the mood.

"Be careful," I said quietly.

"I'm always careful," he gave the standard reply. "You be careful too." He moved towards the door and I knew his visit was almost up.

"Can I at least have a kiss before you go?" I asked, moving in front of the door to block his path.

He put his arms around me and kissed me, lifting me up and squeezing me tight as he turned us around so that he was in front of the door. The kiss took on a life of its own as all kisses we shared seemed to do. John pulled away after a few enjoyable moments and smoothed his hand down my hair again, resting his forehead against mine.

"Get some sleep," he instructed before turning and leaving the room.

Yeah, like that was gonna happen!

Authors Note: Sorry this was mostly just what happened at the beginning of The Seige Part 2 with just a bit of my take on what people were thinking ... next part is where it gets interesting ... promise!


	31. What is it with the military?

**Chapter 31: What is it with the military?**

Dr McKay and Dr Zelenka had successfully installed the new Mark 2 naqahdah generator to the weapons chair platform by mid morning and called me down to assist them in powering it up. I looked at the command chair in apprehension – it looked like a throne crisscrossed with lines in no obvious pattern. Each arm rest had embedded at the end of it something that looked like a gel pack you'd use for a sports injury.

"What do I do?" I asked a bit apprehensively.

"Listen to me very carefully," Rodney's voice was stern and purposeful. "Do exactly what I tell you to do and hopefully no-one will get hurt."

"That's not reassuring me Rodney," I said nervously.

"When you sit down all you have to do is concentrate on powering up the chair -- nothing else, nothing more, nothing but." Rodney instructed. "Don't worry though - it's likely that nothing will happen anyway. Only General O'Neill and Major Sheppard have been able to get a command chair powered up just by sitting in it."

"Okay, so no pressure then!" I carefully lowered myself into the chair, placing my hands on the arm rest pads. Immediately the chair lit up with bright blue light, at the same time reclining me so that my eyes seemed directed towards the ceiling. McKay and Zelenka looked at me in astonishment; Rodney bent his head down, looking at various readouts on his laptop.

"Good. Good. Good. And ... oh no." Rodney said with a sick look on his face.

"What? Did I do something wrong?" I asked nervously.

Without replying, Rodney pulled the connecting cable out of his laptop and ran out of the room. Zelenka walked over to me with an apologetic look.

"So, see? Nothing to worry about."

I was about to respond when Rodney walked back into view and told Dr Zelenka to get me out of the chair, before turning and hurrying away again.

"What was that all about?" I asked, grabbing the hand Dr Zelenka held out to me to pull me out of the chair. The chair powered down as soon as I was no longer sitting in it.

"I have no idea," Zelenka admitted, "but with Rodney this is not unusual."

"I'll just go make myself busy somewhere else then," I said. "Call me if you need me back here."

My first stop was to check in with Teyla and see if she had time for another 'Wraith mind control' training session that afternoon. Apparently Colonel Everett had asked her to stay out of the way and she was more than happy to help me right there and then.

Our session went well – after a couple of hours I was able to fully block her attempts to take over _and_ I didn't have anywhere near as big a headache as I'd had the first time. I felt confident that if I had to I could get what I needed from the Wraith without giving them the chance to take me over. I shared a surprisingly (given the dire situation we found ourselves in) enjoyable dinner with Teyla that was marred only by the absence of Major Sheppard. I hadn't heard from him all day and could only assume his new duties with Colonel Everett were keeping him too busy to leave time for anything personal.

It was late evening but I wanted to see Dr Weir before I turned in about the possibility of telling Colonel Everett of the Wraith weapon room. She was looking at something with Rodney in the control room and I hesitated to interrupt.

"Sabina," Dr Weir noticed me before I could make a quiet exit.

"Dr Weir," I hesitated. "Do you have a minute?"

"Come to my office," she gestured for me to precede her from the control room.

"I can guess what this is about," Dr Weir pre-empted me, "and I don't think now is the time. The warheads were detonated by a meteor field sent by the Wraith, and our sensors have been blind for hours."

"Then wouldn't the Colonel be looking for other options?" I asked, feeling a bit sick that the big plan to defend Atlantis had been so easily thwarted by the Wraith.

"The Colonel is a man who seems ... committed to his own course of action," Dr Weir said diplomatically. "His ego has suffered a major blow here - I don't think he'd be receptive to a civilian coming in with a different plan to defeat the Wraith."

"What is it with the military?" I cursed their attitude that suggested civilians could never come up with something as good as their own plans.

"Aren't you involved quite ... closely with 'the military'?" Dr Weir teased me.

"That makes me uniquely qualified to comment," I said cheekily, not minding her reference to my relationship with John. "Will you at least promise to bring up the Wraith weapon if the timing seems right?"

"That I can do" she agreed. "Thank you for your help with the command chair this morning," she said, changing the subject.

"No problem," I said. "What was that all about anyway? Rodney just ran out of the room without telling me anything."

"The chair is almost out of drones," Dr Weir frowned. "The remaining drones will help us in the short term but it won't be enough to take out a hive ship."

"Is it just me or does it seem to you like everything is deliberately working against us?" I asked in frustration.

"It does seem like that," Dr Weir agreed. "We have to remain positive that the Daedalus will arrive in time to help us."

Before we could say anything else an alarm sounded from the control room and Elizabeth ran from her office to see what was happening. I followed her into the control room in time to hear that the first waves of Wraith darts were heading for the city.

It was all bustle and activity after that announcement. I lingered in the control room trying to stay out of the way as teams deployed at the rail gun positions went into action. I knew that Major Sheppard would be in the command chair trying to make the most of the last drones. Within minutes it was all over, with the last Wraith dart destroyed by the last drone. Although there was a sense of relief that we had survived the first attack there was also a sense of dread. Many of our resources had been used already and it was a sure thing that those hive ships could send down hundreds more darts than we could ever defeat, especially now we no longer had drones to help us.

With nothing else to do I went back to my room to try to get some sleep, hoping that John was doing the same.

Authors Note: I hope you all forgive me for taking license with the chair scenes - I know Carson did that BUT he hated it and Sabina was much keener to do it instead! Lots happening in the next chapter!


	32. Back at you

**Chapter 32: Back at you.**

I was much relieved early the next morning to find John having breakfast in the commissary. His mood was sombre – even if nothing else had, that would certainly have convinced me of the seriousness of our situation.

"Did you get any sleep?" I asked, not really sure what to say to him.

"Some," John said. "Sorry I didn't catch up with you yesterday."

"I didn't expect you to," I excused. "I'm surprised you're even taking the time to eat."

"Orders," John admitted. "I've got to report to Colonel Everett in the control room in a few minutes – somehow we have to come up with a new plan because the old one is dead in the water."

"What about ..." I began, intending to suggest he reconsider the Wraith weapon.

"Don't," John interrupted me, holding up a hand. "I know the kind of leader Everett is and he'll never go for it – too uncertain."

"What's the harm in making him aware that it's an option?" I persisted.

"We're not that desperate yet," John said.

"We have _two_ Wraith hive ships less than a day away and we're down to a few rail guns – I can't see how we're gonna get much more desperate than this!" I exclaimed.

"Yeah, well if the hive ships get here and we still don't have a plan then I'll consider the Wraith weapon," John said it in such a way I knew he didn't believe that time would ever be upon us.

We continued our breakfast in silence and all too soon our brief respite was over. John stood up to leave but hesitated with a look that said he wanted to ask me something but didn't know how to do it.

"Would you consider heading out to the alpha site this morning?" he asked after a few seconds pause. I could tell he found it hard to ask me that question and so I gave it genuine thought before replying.

"If I feel like there's nothing I can do and that I'm just in the way here then I'll consider it," I offered. "I'm not promising anything though because I'd much rather stay here, no matter what the danger."

"Okay," John agreed. I expected him to head out but again he seemed to hesitate.

"What is it?" I urged him to get whatever it was off his chest.

"You ... ah ... you know how I ah ... feel, right?" John rushed the words out quickly, looking at the ground rather than at me.

"Don't," I protested, not even acknowledging his statement. "You are _not_ gonna do some kind of last breathe confession here – everything will work out and then you'll just be regretting it later!"

"I won't regret it," he said with firm surety in his voice.

"Yes you will," I insisted. "When this is all over, if you still want to tell me whatever it was you were trying, badly I might add, to tell me you can do it then."

"Fine," John agreed in amusement. "I have to go ... remember what I said about the alpha site." I was surprised when he bent down and pressed a hard kiss on my lips before turning and walking away. I didn't even bother to look around and see who'd witnessed that – I just sat and watched him go.

"John?" I couldn't resist calling out just before he got to the door. He turned back to look at me with a raised eyebrow.

"Back at you," I said quickly. He grinned before turning away and disappearing out the door.

I really did intend to consider the whole alpha site evacuation thing but it turned out I was needed after all. I got a call from Dr McKay an hour or so after John had left for his meeting – they needed my help in the chair room.

"Sheppard came up with the brilliant idea of using remote flown puddle jumpers to deliver bombs to the hive ships," Rodney told me as I rushed in the door. "We need to get the chair and the jumper to talk to each other so Sheppard can use the chair to deliver the bombs when the time comes."

"How come John isn't here to help with this himself?" I asked worriedly.

"Because he's off with the Marines and Teyla's people chasing the Wraith that beamed down to the city last night during the attack," Rodney said distractedly, setting up his instruments.

"How many?" I asked sickly, glad I'd been maintaining my sensor block nonstop since I'd begun my practice with Teyla.

"Between 20 and 30," Dr Zelenka admitted. "Internal sensors are still down but don't worry – Major Sheppard has the portable sensor units and they're working fine."

_Don't worry?_ Clearly these guys were more than just exhausted if the thought of 20 or 30 Wraith in the city didn't worry them!

"Are we ready to do this?" Rodney asked impatiently.

"I'm ready," I said, trying to put the thought of John being in danger to the back of my mind. I sat down in the command chair more confidently than I had yesterday, in part because I knew it was out of drones and I couldn't do any damage even if I wanted to. The chair lit up immediately and reclined.

"OK, we're in business," Rodney said. "Head down to the Jumper Bay," he told Zelenka. "Radio me when you get there."

Dr Zelenka rushed from the room, leaving me alone with Rodney.

"Is this gonna work?" I asked him quietly.

Rodney walked round to the rear of the dais the chair was mounted on and pulled open an access panel, ignoring me completely.

"Rodney!" I said his name a little louder.

"What?" he questioned me impatiently, looking up from whatever he'd been tinkering with.

"_Is ... this .. going ... to work?_" I spaced each word out clearly as though talking to a child.

"I am exhausted and starving!" Rodney excused his grumpy behaviour. "The military come in here with their big guns and even bigger plans and when they screw it up they turn to the scientists to fix things!"

"RODNEY!" the irritation in my voice must have gotten through to him.

"I don't know, okay!" he admitted impatiently. "It should work ... if we can stabilise the connection between the chair and the jumper and if the power holds out ... and if people give me a chance to concentrate instead of asking useless questions!"

"Thank you," I said, ignoring that last comment.

It took a long time, most of the day in fact, but it was a pretty easy day for me. All I had to do was sit relaxed in the chair while I waited for Rodney to ask me to do something. Zelenka was obviously tinkering with things in the puddle jumper too because every now and then there'd be heated discussion between the two of them as they argued the best way to resolve the problems that kept cropping up. Eventually Rodney and Dr Zelenka seemed ready to proceed with a full test.

"Okay, give it a test," he told Dr Zelenka.

"Standing by," Zelenka's voice came back over the radio.

Rodney stood up and walked over to a control panel. "Sabina, I need you to clear your mind and think about the Puddle Jumper. Think about bringing it online."

I nodded, concentrating hard on trying to imagine the puddle jumper controls coming on line. It took me a few seconds to work out how to do it as I was now attempting to talk to two independent Atlantis systems at the same time. There was a short pause before Dr Zelenka reported back to us.

"Yes! Yes, yes, yes! Rodney! Rodney! It works!" he cried in excitement.

"Thank God!" Rodney sighed in relief. He sank down in exhaustion, sitting on the edge of the dais and closing his eyes. That was lucky for me because he didn't see the delighted grin on my face or the 'light bulb going off' look on my face. If I ever got the chance to use the Wraith weapon I now had a way to help me control the power build up I'd experienced the first time I'd tried to use it.

I think Rodney had actually dozed off before Elizabeth's voice coming over the radio jerked him awake.

"This is Weir. I've got the prototypes," she reported.

"Prototypes. Right," Rodney said wearily. He stood up and walked away, leaving me still sitting in the chair. This time he didn't come back.

Authors Note: Ditto to my comment from the last chapter - plus had to have a reason for Sabina staying on Atlantis. Not much to go now!


	33. The Wraith hive ships are approaching

**Chapter 33: The Wraith hive ships are approaching the planet.**

It was late and I had little hope that I'd be seeing John or Teyla that night. I'd been thinking all afternoon about the Wraith weapons room, what Ancient Elizabeth had said to me, what I'd learned from all my translations and research, and even about how I'd ended up here against all the odds. I knew now that no order was going to come down from Colonel Everett or Dr Weir sanctioning me to attempt to use the weapon to defend Atlantis. If the weapon was going to be of use then it would be up to me and me alone to make it happen.

So instead of heading to my quarters to sleep, putting my future solely into the hands of a couple of remote controlled puddle jumper bombs and the Daedalus that might not even arrive in time, I picked up everything I would need for an extended stay and headed down to the Wraith weapon room. I was conscious of the fact that, since I hadn't heard anything for some time, there could still be Wraith at large in the city. I took the risk and dropped my sensor block temporarily as I made my way down to the depths of Atlantis – hoping I'd be able to sense any Wraith before they were upon me. As soon as I arrived at my destination safely having sensed nothing out of the ordinary, I slammed my block back into place – I didn't want the Wraith to sense what I was doing and I didn't want to appear as a lone life sign when the internal sensors finally came back up.

The next few hours would be a waiting game for me as there was nothing I could attempt until the hive ships had actually arrived at the planet. I tried to sleep but gave it up as impossible and instead spent the night reviewing all the notes I'd brought down with me, trying to convince myself that I was right and that the weapon really would do what I believed it could do. To be honest, if not for the live confessions of Ancient Elizabeth, I don't think I'd have been quite so confident.

I don't know how long it had been before I heard the first news on what was actually going on outside my little room.

"This is Everett," his voice came over the city wide radio. "Jumper Four has just informed us the Wraith hive ships are approaching the planet. Defence team to your positions."

I felt a rush of panic sweep over me ... it was nearly time for me to act and suddenly I felt very nervous, very alone, and very scared.

"This is Weir," Elizabeth's voice followed some seconds later. "Now I know how tired you all are, and how much we have asked of you these past few days. Hopefully the Daedalus will arrive soon, but until that happens our fate is in our own hands. If, during the course of this battle, our mission fails, I will give the order to evacuate. Now, we all hope it won't come to that. But if it does, don't hesitate. That is all."

I wasn't sure what I was going to do if the order to evacuate _was_ given because I was a _long_ way from the Gateroom. I could only hope that they'd scan for life signs so that I could let my sensor block go and they'd know I was on my way. Trying to think positively, I decided it didn't matter because the Wraith would be destroyed one way or another and we wouldn't need to evacuate.

I'd brought my radio so I could hear what was going on – at least what was going on that was taking place over the radio system. I needed to know what was happening so I'd know if, and when to act.

"Sheppard, are you ready?" Dr Weir's voice was steady. I knew that John would be in the control chair ready to remote fly the puddle jumpers but there was no answer. I waited anxiously and a few seconds later Dr Weir spoke again. "They're sending in another wave! Major, we need to go!"

"Rodney," it was Zelenka's voice this time. "Nothing is happening!"

"Why are there no Jumpers in the air?" Dr Weir questioned impatiently.

"We must have exhausted the Mark Two's energy output," Rodney's voice echoed with horror. "It's dead."

I knew exactly what would happen next. John would realise the bombs couldn't be delivered remotely and he'd do the big hero thing and fly one to a hive ship himself. I had only a few minutes to do something before he'd be at the jumper bay and it would be too late.

I rose and stood before the hand controls on the weapon. Taking a deep breath I closed my eyes and concentrated on putting my mind within the weapon _before_ I touched it. The next step was for me to drop my sensor block so that I could link in with the Atlantis power control systems using much the same method as I'd used to get the chair to talk to the puddle jumper. Taking another deep breathe I slowly lowered my hands until they were just touching the hand slots.

I felt that same surge of power from the weapon I'd felt the first time but this time it was routed through the city's power control system before it could build up. I had to take a couple of systems off line so I wasn't surprised when I heard Dr Weir's voice over the radio.

"Sabina?" she demanded. "What are you doing?"

"What needs to be done," I replied shortly, maintaining my control, waiting for the power levels to build up sufficiently to activate the weapon. There was a pause before a different voice came over the radio.

"I am _ordering_ you to stop what you're doing!" Major Sheppard's voice came through loudly. I felt relief that I'd stopped him for the moment from making that suicide flight in the puddle jumper.

"I'm no longer under your command, remember?" I said lightly, most of my attention still on the power levels.

"This is a military situation," John pointed out, "so technically _everyone_ is under military command. You've cut power to the jumper bay – I need to get in there _now_ before the Wraith send too many darts for us to handle!"

"You mean so you can fly the bomb into the hive ship and blow yourself up in the process?" I said angrily. "You said we weren't at the stage of being desperate enough to try using the weapon ... well guess what? Now I'm _that_ desperate!"

"Sabina, please don't do this," John tried to reach me on a personal level.

"Too late," I replied, taking the final step and reaching out my mind to the Wraith like Teyla had taught me.

There were so many Wraith darts flying over the city that it was almost too easy for me to make the connection. I saw Atlantis through the eyes of the Wraith as they hurtled towards us. I could feel their hunger and malevolence, their overwhelming desire to take the city so they could reach their rich new feeding ground. The power of the connection was so much more than I'd been able to achieve with Teyla and for a few moments I was overwhelmed in the rush of sensations.

It was too much and I knew I was in danger of giving control to the Wraith if it went on much longer. I could feel my body shaking as I struggled to make sense of what I was getting and separate that from what I needed to feed to the weapon. As I began to lose my focus random thoughts started flashing through my consciousness. Atlantis – the home I'd been looking for my whole life and somehow stumbled across. Learning to fight with Teyla and getting my arse kicked every time. Running down the corridors in the early morning as I struggled to keep up with John.

_John_ ... oh God ... multiple images of the time we'd spent together raced through my mind. My struggle became just as much about controlling my emotions as it was about controlling the power of the Wraith connection.

How pissed off was John going to be with me if I messed this up?! That one thought alone gave me the strength to pull everything back inside and refocus my efforts on tightening my connection to the Wraith. It was the hardest thing I'd ever done but slowly I managed to silence my thoughts and concentrate only on the Wraith. Once I felt that I had enough control I turned my attention back to the weapon and slowly tried to transfer that connection to the weapon. It was about timing as much as anything, coordinating the exact moment when I should take myself out of the middle leaving only a direct connection between the Wraith and the weapon.

I was sure that this was the way to make the weapon work but when I tried to take myself out of the loop I found I couldn't release without severing the link. With a sick feeling I realised I would have to maintain the link which meant I'd still be connected to the weapon when it activated. Praying that John would forgive me for what I was about to do, I released my hold on the power control systems.

Power slammed into the weapon with tremendous force. The blocks that controlled the weapons frequency setting began to move, shifting up and down in an almost graceful dance before finally coming to rest in a pattern of highs and lows. The room began to shake as a gap appeared in the ceiling directly above the weapon. The gap widened and I caught a glimpse of the blue sky over Atlantis – for some reason that fact struck me as strange because it felt like a lot more time had gone by than was actually the case. A visible energy dome gathered around the weapon, encasing me within it. The energy dome spread up the shaft, travelling at a steady rate. When it hit the top of the shaft I felt the power peak and the wave detonated, spreading out in all directions as it flashed through the city and out into space.

The concussion from the wave's dispersion sent my body hurtling away from the weapon and I saw myself crash into the opposite wall and lie still.

"JOHN!" I heard myself screaming in my head when I tried to wake up but couldn't. "JOHN ... HELP!"

I lost awareness for a few seconds but my attention was reclaimed when Dr Beckett and a medical team came running into the room. It had only taken a few minutes for him to get there and I could only assume that Dr Weir had ordered a medical team as soon as she'd realised what I intended to do.

Dr Beckett knelt beside my body and felt for my pulse ... immediately he called for the defibrillator and for someone to bag me. I watched as they hooked me up to the monitors and shocked me. No pulse. Again. Still no pulse. They continued to push breath into my lungs and then shocked me again. I could see the expression of grief on Dr Beckett's face as he asked someone to call it before rising slowly to his feet.

"I'M NOT DEAD!" I tried to scream but of course no one could hear me. Was this what being dead was like?

I thought that things were as bad as they could get ... until Major Sheppard arrived. He took in the situation with a single glance and I saw him visibly steel himself before he questioned Beckett.

"Carson?" his voice held the faintest edge of shakiness.

"I'm sorry," Dr Beckett said sadly. "There was nothing we could do."

"No," John almost whispered the words. "She's _not_ gone – I can feel it."

"There's no pulse Major," Dr Beckett told him reluctantly. "Sabina was gone before we got here."

"But I _heard_ her," John protested. He seemed to lose the strength in his legs as he slipped down against the walk and sat on the floor across from my body. "She called out to me ... called me for help."

As I watched John bow his head over his knees I realised what he'd said. He'd heard me call to him even though I was pretty sure that I'd never managed to verbalise my plea.

"JOHN," I yelled. "CAN YOU HEAR ME?"

"Sabina?" John raised his head suddenly and looked across at my body. A pained expression crossed his face as he was bombarded with the image of my supposedly dead body. I could see him swallow hard to contain his grief as he lowered his head again.

"JOHN," I yelled in exasperation. "IF YOU EVER WANT TO ENJOY A MOMENT OF SILENCE AGAIN YOU BETTER PAY ATTENTION TO ME RIGHT NOW!"

"Sabina!" John cried, jumping to his feet and looking at the weapon.

"Major?" Dr Beckett put a hand on John's shoulder, clearly thinking that he'd lost it in his overwhelming grief at my demise.

"It's all right Carson," John insisted. "I can hear Sabina – in my head. She's still here and she ..."

"ENOUGH CHIT CHAT!" I broke in to John's thoughts, not really caring at this point if Carson thought he was crazy. "I NEED YOU TO TRUST ME AND DO EXACTLY WHAT I SAY. YOU NEED TO PLACE MY HANDS BACK ON THE WEAPON. HURRY!"

John moved over to my body, carefully picking me up and carrying me over to the weapon. He placed my hands gently over the controls. "What now?"

"YOU NEED TO TOUCH THE WEAPON – BUT MAKE SURE YOU HAVE ONE HAND ON ME AS WELL. DON'T WORRY – IT'S PERFECTLY SAFE," I instructed.

John did exactly as I said without any hesitation. "Nothing's happening," he said worriedly.

"I _KNOW_ ... YOU NEED TO IMAGINE YOURSELF AS A BRIDGE ... A BRIDGE BETWEEN THE MACHINE AND MY BODY ... THEN BRACE YOURSELF BECAUSE I'M GONNA BE TRAVELLING THROUGH YOU TO GET BACK TO ME. I DON'T THINK IT'LL HURT BUT IT MIGHT BE ... A LITTLE UNCOMFORTABLE."

"You don't _think_ it'll hurt?" John questioned me incredulously.

"JUST DO IT! I DON'T HAVE A LOT OF TIME HERE!" I retorted.

John closed his eyes and a frown appeared on his face as he concentrated on doing what I'd asked. I saw the bridge appearing in front of me ... a wide path with simple trellised sides, glowing with ancient light. I stepped hesitantly onto it and when it held my weight I moved forward confidently. As I walked forward the scene changed and instead of walking on a bridge I felt myself falling ... falling into John's mind. I landed hard as though I'd jumped from a fair height and felt John flinch. Catching my breath I looked around in amazement – was this what John's mind was like every day? I found myself walking through a field with long grasses gently swaying in the breeze. The sun was shining down warmly and the sky was an impossible blue. I walked slowly through the field, running my hands over the tops of the grass before spotting another bridge up ahead.

This one was made from a beautiful red brown wood that almost glowed in the sunlight. The sides of the bridge were crisscrossed beams and there was a scalloped banister to rest my hands upon. The whole thing was carved with intricate designs and sanded so that it was as smooth as silk. Where the first bridge had looked ethereal and temporary this one looked solid and stable, giving me the impression it would be there when Atlantis itself had turned to dust. I stepped out onto the bridge and began walking slowly across, looking down to the gentle river than flowed beneath it. As I neared the other side I felt that same shift in scene and I was falling again ... falling into myself.

I opened my eyes and saw my hands sitting on the weapon, John's right hand resting over mine while his left was placed firmly on the machine. Leaning back slightly I felt the comforting strength of his entire body pressed into mine.

"John," I whispered tearfully.

"You know," he said with a relieved grin. "You didn't have to shout."

"Sorry," I slurred, before I fainted back into his arms.


	34. Thanks for saving mine

**Chapter 34: Thanks for saving mine.**

My first conscious thought was the realisation that someone was holding my hand. I opened my eyes and discovered I was in the infirmary again and that it was John sitting beside my bed, one hand resting over mine.

"Hey," I croaked, trying to squeeze his hand and discovering how weak I was when all I could manage was the movement of my fingers within his.

"Hey yourself," he replied with an easy tone that did little to cover the seriousness in his whole demeanour. "You scared me," John said, looking away and swallowing hard. "Don't do it again."

"Not planning on it," I agreed tiredly. "Did it work?"

"Spectacularly," John admitted. "From the reports I've been hearing the Wraith hive ships, the darts, the Wraith themselves disintegrated instantly into ... well the best description I've heard is little mounds of funny coloured sand."

"Sweet," I smiled triumphantly – that was more than even I'd hoped for. "I'm not gonna say I told you so."

"You risked your life," John said, ignoring my last comment. I realised that although a large part of him was just relived to have me alive when he'd believed me dead, another part was angry that I'd defied his orders so blatantly. "I could just as easily have been arranging your memorial service!"

"I didn't do anything that you weren't willing to do yourself!" my voice came out a lot weaker than I would have liked and I felt tears welling up from deep inside. I looked away and swiped angrily at my eyes.

"It's not the same!" John insisted. "Part of my job is being willing to make the ultimate sacrifice to protect the people I've been made responsible for ... to protect you."

"What, so me being willing to do the same doesn't count because I'm not _military_?" I asked incredulously, forgetting my tears for a moment at the absurdity of that view.

"I know that you closed the jumper bay deliberately," John looked at me closely. "Rodney's been trying to get the sensors back on line – he worked out that you didn't need to do that to take control of the power systems."

"So I didn't let you go out and splatter yourself all over the inside of a hive ship," I retorted sarcastically. "Are you going to send me to the brig for that?"

"You are the most ... stubborn ... annoying ... _stubborn_ woman!" John complained in exasperation. "We shared an experience that was ... well I don't even know how to describe it, it was that deep ... and you're _arguing_ with me?"

"Hey, you started it with your 'I can risk my life to save you but you can't do the same for me' speech!" I passed the complaints straight back to him. I wanted to argue some more but the enormous headache I'd been expecting chose that moment to arrive, sending searing pain through my skull. I winced and clamped a hand across my forehead like that would help somehow.

"What's wrong?" John's anger was forgotten in his concern for me.

"Headache," I gasped. I spaced out for a bit, coming back to myself when I felt the injection in my arm. John must have gone to get Dr Beckett, dobbing me in for a needle which he knew I hated.

"I told you not to upset our patient," Dr Beckett scolded John. "She's still very weak even if she's putting on a good act to convince you otherwise."

"I'm fine," I insisted.

"You're NOT fine!" two voices chorused back at me. I don't know what would have happened next if John hadn't been interrupted. He turned away and activated his headset.

"What is it Rodney?" he asked. He listened for a moment before responding. "Okay, I'll be right there."

Turning back to me, he reached out and put his hand across my forehead. The sensation of his cool hand was soothing and I wished he could just stay there like that, even though I knew that duty called.

"Do what Carson says," he told me sternly. "I'll be back to see you later."

"Okay," I agreed. I watched him walk towards the door, waiting until he was almost there before I called out to him. "John!"

"Yeah?" John turned back to look quizzically at me.

"Thank you," I said simply.

"For what?" he frowned.

"For saving my life," I acknowledged.

"Yeah, well," he said, shifting uncomfortably from one foot to the other. "Thanks for saving mine." Not waiting for my reply, he turned and left the room.

"Try to get some rest," Dr Beckett laid a hand on my shoulder, which is when I realised something.

"I didn't get the jolt," I said it worriedly. "You know ... when someone with the natural gene touches me. I only just realised – even with John I didn't feel it."

"I'm not surprised lass," Dr Beckett dismissed my concerns. "You overloaded your system as far as anyone can ... you're lucky to be alive! Don't worry," Dr Beckett reassured me. "I'm sure all your ATA gene powers will be back once you've given yourself the chance to recover. Now I suggest you get some sleep."

That wasn't a hardship ... I was so tired I'd been finding it hard to concentrate on anything even before the end of John's visit. I drifted off to sleep, wondering at the back of my mind what it was that Rodney had wanted to see John about.

I woke up briefly some hours later, ripped from sleep by the sound of my own voice calling for John. Dr Beckett must have been close by because he appeared at my side only moments after I'd awoken.

"Where's John?" I asked in confusion, still half asleep and not sure of where I was.

"Major Sheppard was back to visit you a few hours ago," Dr Beckett admitted. "Unfortunately he had to go on a mission but he said he'd be back here as soon as he returned." Dr Beckett busied himself talking lots of readings and writing things in his chart but I hardly noticed.

"What mission?" I frowned.

"He asked me not to tell you," Dr Beckett admitted. "Your only priority is getting better. Major Sheppard will be back before you know it and you can ask him about it then."

Doctors were too good at keeping secrets so I resigned myself to the fact that I wouldn't be getting any more information out of Carson. I tried to stay awake to see if I could overhear anything that would explain it but I must have drifted asleep only moments later because when I next work up I couldn't remember hearing anything.

Hours later I awoke again, feeling so much better I was almost ready to leave the infirmary – if all I needed was sleep then surely I could do that in my own quarters? Dr Beckett denied my request to be discharged but did let me sit up reclined in my bed. I looked around and was dismayed to see the number of occupied beds. I knew there would have been injuries and even casualties from the Wraith attack – the time it took to activate the weapon was unknown to me but I knew it would have been more than a few minutes.

I was drifting in a sort of half dose, thinking over the events of the past few days, when I saw Dr Weir and Teyla come in to the infirmary. They both stopped at my bed to tell me they were glad I was okay before moving along to another bed across the infirmary. Aiden was lying on that bed with his eyes closed, wearing a bizarre-looking pair of sunglasses. A scanner was moving back and forth alongside his bed.

"It's starting to affect his brain chemistry," Dr Beckett said softly.

"There's no way you could have known that, Carson, and its better this than death," Dr Weir excused.

"We need to be more aggressive -- wean him off it quicker than I expected to," Dr Beckett advised. "It'll be painful and arduous, but I think it may be the only option. I've sedated him, but he should definitely be under secure supervision."

"I've already stationed a guard at the door," Dr Weir admitted.

"Doctor Weir -- the Daedalus is requesting permission to land on the east pier," a voice reported over the intercom.

"Permission granted. We'll meet them there," Dr Weir said as she and Teyla turned to leave the room. I really wanted to find out what had been going on but Dr Beckett refused to let me leave. To be honest I felt a bit neglected – I'd practically saved Atlantis and all they could do was relegate me to the infirmary and not even bother to tell me where things were at!

I tried to console myself with the thought that things couldn't be that bad - with the Daedalus here Atlantis would have a shield, should there be any fallout from us taking out three hive ships. That worked for an hour or so and then I couldn't stand it anymore. No one was paying attention to me and when an opportunity presented itself, I snuck out of the infirmary.


	35. I simply realised my place

**Chapter 35: I simply realised my place.**

I slipped down the hall and made it to my room without drawing anyone's attention – not bad for someone dressed in a hospital gown. I changed and tried to make myself look presentable – a hard task once I'd got a look at myself and seen a very pale face with bruised circles under the eyes that I hardly even recognised as my own. Realising it wasn't going to get any better, I made my way up to the control room.

My timing was perfect because Dr Weir, Major Sheppard, and another military man I didn't recognise were all standing near a console while Dr McKay was checking one of his readouts.

"The shield's holding under the bombardment but it's under incredible strain," he reported.

"How long will it hold?" Dr Weir questioned.

"Well, if they stop firing at it," Rodney said almost snidely, "it'll last almost indefinitely but ..."

"Are we talking months, weeks?" Dr Weir persisted

"Days," Rodney admitted sickly. "At this rate the ZedPM will be depleted within days."

That was the moment when John noticed my presence. "Sabina?" he questioned. "Should you be out of the infirmary?"

"So this is the lady we have to thank for taking out those two hive ships?" the other man broke in to ask before I could respond.

"This is Sabina Scott," John introduced me. "Sabina, this is Colonel Caldwell, commander of the Daedalus."

"What's going on?" I looked at John, hardly aware of the tremor in my voice. "Are there more hive ships?"

"I'm sorry Sabina," it was Dr Weir who answered me. "Maybe I should have sent someone down to brief you ... but we felt the best thing we could do was let you regain your strength."

"How many?" I looked at John again, willing him to include me in the decision on what was to be done.

"Ten," he admitted. "There were twelve but we took the Daedalus out after them and destroyed two with a site to site bomb transport - before they worked out what we were doing and found a way to block us."

"Rodney, what's the status of the Wraith weapon?" I asked, hoping my voice sounded stronger than I felt.

"I already thought of that," Rodney admitted, not looking at John to see his reaction. "It's fried – you were lucky the thing had enough power to ... you know ... get you back to yourself. It's not an option."

"But couldn't you rig up a different power source?" I asked incredulously.

"Maybe, maybe not," he said. "The whole thing is a bit of a black box and I'd need a lot more than a week to even figure out how it works. Maybe the ancients only meant it to be used once – maybe the plan was to find a way to take out the entire Wraith in one go."

"Oh," I said quietly, looking down at my feet. I knew the chances of my being able to operate the weapon successfully would have been slim given that I'd still not recovered the full use of my ATA gene. But to be told there was no chance at all because I'd _broken_ the weapon filled me with both guilt and despair.

"Dakara!" Colonel Caldwell suddenly exclaimed. When he was greeted by blank looks from all of us, Caldwell continued. "Just before I left, the SGC managed to wipe out a race called the Replicators. They did it with an ancient weapon that sounds very similar to the one Sabina used. One of the G'oauld, Baal, found a way to get the Stargates to progressively dial each other throughout the whole galaxy just before the weapon fired. The effect travelled through the Stargate system wiping out the replicators on every planet and in space."

"That would have been nice to know up front!" Rodney complained, shooting a glance in my direction.

"You mean we could have wiped out _all_ the Wraith?" I asked sickly. "If I'd waited to use the weapon ..."

"Not all of them," Major Sheppard pointed out. "Only those on, or in orbit around planets with a Stargate. That wouldn't include the armada heading for us right now."

"Not in time either," Caldwell added. "Only Baal knows how to reprogram the Gate – even Colonel Carter couldn't work out how he did it. We never would have figured out how to do it with the little time we had left."

"But maybe one day," Rodney said excitedly. "If I can get into the weapon and find out how it works ... I'd need access to Carters research on the altered Gate program ... of course it's only an assumption that the Pegasus Gate system is similar enough that the same thing could work here ... they might have put in fail safes to stop that from happening but we could ..."

"_Rodney_," John interrupted Rodney's babbling, casting a concerned glance in my direction. "You can think about that later ... we need a solution we can implement in a day, not one that could take years."

"Yes, yes," Rodney said apologetically, turning back to his console to take further readings on the shields.

There was a momentary silence during which I realised the futility of my being in the control room. My usefulness as an ATA gene carrier was temporarily zero and the Wraith weapon was out of commission. Sure I'd taken out two hive ships but that was a drop in the ocean compared to the ten hive ships now on their way. If I'd waited then maybe I could have done something about those. But I'd let my personal emotions control me and ended up screwing things up ... again!

"I should ... You need to ..." there was no graceful way for me to take my leave so I just gave up. Looking anywhere but at the occupants of that room, I quickly turned and fled down the stairs.

"Sabina!" I heard John calling after me but I didn't stop. Before I'd gotten halfway to my quarters my arm was grabbed and I was pulled to a stop.

"What was that all about?" John demanded, pulling me around so he could look at me.

"What was what all about Major?" I directed my gaze over his left shoulder and tried to pretend that I felt nothing.

"_That_ – back in the control room!" John refused to let me off the hook. "Why'd you run off like that?"

"I didn't _run_ off," I denied. "I simply realised my place ... which isn't being part of high level discussions about the fate of Atlantis."

"Your _place_?" John asked incredulously.

"Yes, Major," I responded crisply, much as I had during my weeks of basic training. "My place – to activate the ancient technology with no requirement to actually understand it. I think I've proved pretty spectacularly what happens when I forget my place."

"You couldn't have known the weapon would burn itself out!" John said in exasperation.

"Dr McKay would have known," I refused to excuse myself. "I let my emotions direct my actions and now Atlantis is worse off than it would have been if I'd done nothing."

"What about me?" John asked quietly, not believing that I was suggesting I should have let him die.

"The Daedalus arrived in time," I responded flatly. "You would have been rescued before the bomb went off and they would have taken out the remaining hive ships. Then we'd still have the weapon now ... when we really need it."

"You can't know that," John denied. "Besides, it doesn't matter how many hive ships we take out ... they're just gonna keep coming and coming!"

"Don't you have a meeting to be at?" I asked, tugging my arm away from his grasp.

"Dr Weir ordered everyone to get some rest – we're meeting in the morning." John looked at me thoughtfully. "You want to go get something to eat?"

"I'm not hungry," I said quickly, keen to get away so I could think. "Anyway, I didn't exactly have permission to leave the infirmary – I'd better get back down there so Dr Beckett can ream me out about my recklessness."

"I'll walk you down," John offered, surprising me by ignoring the last part of that statement when I'd been sure he'd be angry.

"There's no need Major," my tone was again crisp and impersonal. "It'd just be a waste of your time."

"Let me decide how I want to use my time," John insisted, a puzzled and somewhat hurt look on his face.

"_Sabina_," Dr Beckett scolded me as soon as we arrived in the infirmary. "Not 24 hours ago you were at deaths door – you shouldn't even be out of bed! What were you thinking?"

"I wasn't," I admitting, realising how much my short trip to the control room had taken out of me. I was even grateful for John's hand under my elbow as he guided me across to Dr Beckett.

"Let me check your vitals," Dr Beckett said, helping me up onto one of the examination tables.

"You don't have to stay," I told John when it looked like he was settling in. "I'll be fine."

"I don't know what's going on in your head," John ignored my request. "We need to talk ... but this isn't the time."

"It never is," I muttered under my breath.

"When this is over it'll be number one on my list," John promised. Ignoring the fact that the infirmary was busy and that Carson was standing right there waiting to examine me, John threaded a hand through my hair to grasp the back of my head before pressing a gentle kiss on my lips. Up that close it was impossible for me to avoid his eyes ... in them I could see his confusion and hurt at my distant treatment as well as his firm resolve to fix things. I had no idea what he saw in my eyes but I was very aware of how thinly held my emotional control was.

After pulling me closer for another, harder kiss John stroked his hand down my hair in farewell, turned, and left the infirmary. Once he was gone I raised a shaking hand to my lips, still feeling that tingle of electricity he'd passed to me.

"ATA gene back in operation?" Dr Beckett quipped.

"Oh yeah," I admitted. I sat patiently through my examination and made no protest when Carson informed me that some of my readings were still a little off and that he wanted to keep me in the infirmary for observation.


	36. Prepare for detonation flash

**Chapter 36: Prepare for detonation flash.**

I was curled up in my bed early the next morning, pretending to be asleep when I heard the sounds of a scuffle and then a body falling to the floor. I turned over in time to see Lt Ford run over to a fallen marine and grab his pistol.

"Ford!" Dr Beckett confronted the obviously agitated Lt.

"Don't move or I'll shoot!" he threatened, walking towards Carson, and aiming his gun at him. "Where's the rest of the enzyme?" he demanded.

"There is no more," Dr Beckett admitted reluctantly.

"I saw you extract it -- don't lie to me," Ford protested. "Where is it?"

"No, I'm not lying," Beckett insisted, holding his hands up to Lt Ford in a calming gesture.

I jumped as Aiden suddenly fired the pistol at Dr Beckett, only just missing him.

"Where is it?" Ford demanded again.

"You're not thinking straight, son," Dr Beckett tried to talk sense into him. I admired his calm in what was a very tense situation. The Lieutenant could very well kill him and yet Dr Beckett was still trying to look after Ford's best interests.

"You're all afraid of me," Lt Ford accused, sounding almost childish in his complaint.

"Look at what you're doing," Dr Beckett pointed out incredulously. "We have good reason to be."

"I'm gonna die if I don't get it," Lt Ford accused.

"Aiden, you're not gonna die," Dr Beckett's tone was caring and sure as he tried to talk Aiden down from the tense situation. I thought he was making progress but then Aiden seemed to focus once more.

"Shut up!" Ford yelled. Without taking his eyes off Carson, he slowly and deliberately turned his gun on a man in a wheelchair. Was he really going to shoot an innocent man to get what he wanted? "I'm not gonna ask again," he threatened.

Reluctantly, Carson turned and walked over to a cabinet on one side of the room. He opened the door and took out a bag of brownish looking fluid.

"Is that all of it?" Lt Ford demanded.

"I promise you," Dr Beckett confirmed.

"Toss it over," he instructed. Carson seemed to hesitate and Aiden shouted "Toss it!" Carson tossed it over and Aiden caught it with his free hand. "Don't follow me," he growled before turning and running out of the Infirmary.

Dr Beckett looked sadly after him for a moment before making his way over to the downed marine. After making sure he was all right, Carson instructed some nurses to continue with his care and then hurriedly left the infirmary himself.

Dr Beckett returned only a short time later and informed us of the plan to trick the Wraith into thinking Atlantis had been destroyed by setting off a bomb at the outer edge of the shield before cloaking the city. It made sense – John was right when he'd said the Wraith would just keep coming and coming no matter how many ships we destroyed. I asked Carson quietly what would happen to Lt Ford and was relieved when he told me that Major Sheppard had gone after him. John would be more compassionate than anyone else, especially someone who didn't even know Aiden.

The infirmary became very busy after that, preparing patients for transfer. As many non essential personal as possible would be transported to the Daedalus while the plan was carried out. Dr Beckett tried to get me to be one of them but I still felt that same dread at the thought of leaving Atlantis and convinced him I should remain just in case someone with the ATA gene was needed for anything. Dr Beckett agreed, as long as I stayed in the infirmary so he could keep an eye on me. I was happy to do that, especially once I heard that part of the plan involved Teyla sending a message to the Wraith that we would rather destroy the city than let them have even a tiny part of it.

"Good luck," I said quietly, watching as Teyla lay down on the bed and allowed Carson to hook her up to a monitor.

"Thank you," Teyla replied serenely.

"Now," Dr Becket informed her. "I'm jolting you out of this the second I feel there's a problem."

"I understand," Teyla acknowledged.

"We're all set down here," Dr Beckett reported to the control room over the intercom. We waited patiently for Dr Weir to give the go ahead.

"Doctor Beckett?" Weir's voice questioned just moments later.

"Teyla?" Dr Beckett turned to her with a questioning look.

Teyla took a deep breath, and then nodded. "I am ready," she said confidently.

"We're good to go," Dr Beckett told Dr Weir.

"Alright," Weir responded. "Send our message."

Teyla took another deep breath, then exhaled and closed her eyes, concentrating on making the connection.

"I am on one of the ships. ... They see me," she reported after a few seconds. She gasped, opened her eyes and sat up on the bed, staring straight ahead.

"Teyla?" Carson stood up, looking at her nervously.

"The message has been delivered," Teyla said with a satisfied smile.

"Elizabeth -- it's done," Dr Beckett reported, before sinking back down in relief.

I hadn't realised that I'd become used to the sound of the Wraith bombardment on the shields until it ceased. A few seconds passed and then the city-wide comm. system activated.

"Attention all personnel," Dr Weir announced. "Prepare for detonation flash."

Everyone turned away from the windows as the excessively white light of a nuclear warhead going off flashed through the city. We all waited anxiously to hear if the plan had been a success. It took longer than I would have thought before the city-wide comm. system activated again.

"This is Dr Weir," I could hear the jubilation in her voice. "The Wraith fleet has broken orbit and entered hyperspace. The cloak has been deactivated and for the time being Atlantis is safe."

It was over ... after three weeks of worry, fear and desperation, we had survived the coming of the Wraith. Our loses had been great – in particular Colonel Everett who'd been reduced to an elderly man during an interrupted Wraith feeding, and Lt Ford who'd found a way to take a jumper through the Stargate despite Major Sheppard's attempts to bring him down. Hopefully it would be some time before the Wraith discovered our ruse and returned to try again.

Authors Note: Only one more chapter to go ... the wrap everything up chapter.


	37. This doesn't mean

**Chapter 37: This doesn't mean I'm going to start obeying your orders.**

Now that it really was over I didn't know what to do with myself. I assumed that with Colonel Everett out of the picture John would again be the ranking officer in charge of Atlantis so he'd be busy tying up all the loose ends. What I really needed was a holiday ... perhaps I could get Carson to fly me to the mainland once all the dust had settled. That wouldn't be an option for a while though because it would probably be days before everyone was recovered enough for things to return to normal.

During the lull between the end of the attack and the return of the Daedalus with the bulk of Atlantis's personnel the city took on the feel of a ghost town. Drs McKay and Zelenka had gone off to get some much needed sleep ... in fact it seemed that most of those who'd stayed behind had retired to sleep. Practically all I'd done for the past couple of days was sleep, so more was the last thing I wanted. In the end my curiosity drew me back to the Wraith weapon room.

I could almost have believed that Rodney was wrong about the weapon being burnt out because on the surface it looked the same as it always had. Regardless of the outcome I felt a strange fondness for the room I'd spent so many hours in. I raised a hand, contemplating trying the controls to see if the weapon really was dead.

"I wouldn't do that," John's voice echoed from the doorway. "I know Rodney is usually right about these things but ... do you want to be the one time he's proven wrong?"

I said nothing in response and John took a step into the room.

"I'm sorry about Aiden," I said, moving my hands away from the console. I kept my eyes on the weapon, aware that John had taken a few more steps towards me.

"So am I," he said sadly. "We tried the planet he gated to but I knew he wouldn't be there. He ditched the jumper and dialled another address we couldn't trace."

"He was always nice to me," I glanced at John quickly before looking away again. "So ... what now?"

"The way I see it," he drawled, "we have two options. Option one we spill our guts, get rid of the anger, have fantastic make-up sex and then live happily ever after."

"And option two?" I asked, fighting the sudden urge to smile.

"Option two," he took another step towards me, "we skip the gut spilling anger and go straight to the make-up sex."

"I'm guessing you're gonna go for option two?" my voice quivered as John closed the distance between us to a single small step.

"See that's where you're wrong," he denied. "I'm actually gonna go for option one and since I'm now back to being the ranking military officer for the time being, I'm not giving you the choice."

"I'm not ready for this," I admitted, appreciating his attempt to lighten the mood between us.

"Who's ever ready for something like this?" John asked incredulously, suddenly deadly serious. "I thought I'd lost you," he reached out a shaky hand and stroked my cheek. "It was ... pain ... deep ... like I've never experienced before. I mean, I'd gotten a taste of how bad it could be when we found you the day you first touched that console," he gestured towards the weapon.

"Rodney said you almost fainted," I admitted.

"I _didn't _almost faint," John denied hotly, drawn into that old debate between him and Rodney momentarily. A silence stretched between us again ... I didn't know what to say ... what was he expecting me to say?

"It weakened me," John admitted. "And I resented it because I thought that made me weak as a leader."

"You resented me," I stated it as though it were fact. "Do you regret getting involved with me?" I asked.

"NO!" John's voice was frustrated. "I never resented you and I would _never_ regret meeting you. There was a connection there from the first day ... you must have sensed it too."

"Yes," I admitted. "Although to be honest I decided pretty early on that it was the ATA gene giving you the push ... I even asked Carson if it was possible because I just can't understand why someone in your position would be interested in me."

"We're not gonna do the whole 'me leader, you nothing' thing again!" John commanded, getting riled up for the first time since he'd arrived.

"I don't see why it makes you angry when I point out what's pretty obvious to everyone else!" I persisted. "I wouldn't be here unless by accident."

"And I wouldn't be here _either_," he threw back at me, "if I hadn't sat in the command chair in Antarctica and accidentally powered it up! I had no more idea about the Stargate program, Atlantis or any of it than you did the first day you arrived."

"That may be," I acknowledged, "but you're a Major in the US Air Force. You're smart; you've got serious 'skills' – you're not just a body that happens to have the ATA gene!"

"You may have been just a body with the gene to start with," John admitted, "but surely you can see that's no longer the case! You're just as smart and you've worked hard to get yourself some equally 'serious' skills. We need you here ... I need you here."

He'd said similar things to me in the past but they'd never penetrated that hard shell I'd held around my heart because deep down I didn't believe them. It wasn't anything different that John said this time that opened my eyes ... but finally I realised that he was right. I _had_ worked hard and I _had_ acquired skills that could only be of use in Atlantis. Even without the possibility of using the Wraith weapon again, I really _did_ belong here! My lips trembled as I tried to stop myself from breaking into tears. Holding a hand against my eyes I turned away from John, taking a few deep breaths to calm myself down. John gave me some time before he redirected the conversation again.

"As I said," John continued. "I thought having such strong ... feelings for you would make me weak. Did I not want you to use the weapon because it was the right call from a military perspective or because I was scared of loosing you? I over analysed every decision and if you'd asked me what my main motivation was I wouldn't have been able to tell you – I _don't_ know if it were someone else in charge that they wouldn't have ordered you to use the weapon and damn the risks."

John waited a few moments to see if I was going to say anything before continuing. "When the command chair didn't fire up and I realised what I'd have to do I also realised something else ... those feelings I had for you didn't make me weak. They gave me the motivation to do what had to be done and the surety that it _was_ the right thing to do –because I was doing it for you and not just because it was my duty. That's when I admitted that my orders not to use the Wraith weapon were as much to do with not losing you as they were about the outcome being too unpredictable to justify the risk."

"I was angry with you," I admitted. "I thought you wouldn't let me try the weapon because you didn't think I was up to it – that I _couldn't_ do it. It just made me even more determined to prove you wrong. That wasn't the only reason why I did it but I'd be lying if I said it didn't factor into my decision."

"I was angry with you too," John rubbed a tired hand across his eyes. "To be honest I'm still angry – you took a risk, not only with yourself but with everyone on Atlantis. You disobeyed my direct order because you decided you knew better than everyone else. I understand the sentiment – we both know I've been there myself! I do understand the thinking when the lives of people you care about are at stake and you're convinced the person in charge is wrong. I've acted on that thinking more than once and I never regretted it."

"So why are you angry then?" I said, confused now about what he was trying to tell me.

"Because you didn't trust _me_," he said hotly. "Not Major Sheppard the leader, but John the person. You were supposed to feel closer to me than anyone else on this base and yet at every turn when it was time to trust me you deliberately disobeyed me!"

"It wasn't like that," I protested. "I..."

"I wasn't finished!" John interrupted. "I know I made it impossible for you – you tried to talk to me to convince me about the weapon but I was too caught up in worrying about your safety. I didn't want to hear a logical argument if it meant I'd have to reconsider my military decision."

"We were both wrong," I admitted. "You should have given me the chance to convince you but I should have considered what you were saying too. I didn't want to hear your logical arguments either because I saw that weapon as the reason I was here and the only way to prove that I belonged here."

"I stuffed it up, didn't I?" I turned away, feeling my eyes begin to brim with unshed tears. "One day we're gonna need that weapon and we won't have it because of me." A few tears ran down my face and I angrily brushed them away.

"You didn't stuff it up," John denied. "Hell, even the Ancients couldn't work out how to use the weapon to get rid of the entire Wraith all at once – that's probably why they never activated it themselves."

"Do Dr Weir and Rodney feel the same?" I asked, despite the fact that it really was pathetic I cared so much what they thought.

"Rodney finally found something useful in that weapons research inventory gizmo you activated way back – he said the weapon had never been tested and it's a wonder you even got it to work once. He's already rubbing his hands together at the thought of how much of a genius he's gonna look when he fixes it where no one else could," John said only partly in jest. "As for Elizabeth, she firmly believes that casualties were much less as a result of your setting off that weapon when you did. Since I would have been one of those casualties I whole heartedly agree."

"You know I did it for you," I said, more tears escaping as emotions churned inside me. "I'd like to say the lives of everyone on Atlantis were at the forefront of my mind but the timing kind of gives that away. In the end I just couldn't let you die if there was anything I could do about it."

"I know," John raised a hand and brushed at the tears tracking slowly down my face. The intent look on his face made it clear he was thinking about my motivations and I wasn't ready to start confessing my feelings just yet.

"Is there anything else you're angry about?" I asked before he could say anything else.

"I wouldn't say angry," John let me get away with redirecting the conversation. "Frustrated ... that's a better word. You were always so careful to maintain a little distance between us and every time I tried to get closer to you something happened to pull you away. I felt like I was trying to build a bridge over a river when I only had access to one side."

"Did you see me?" John's mention of bridges had reminded me of something I'd been meaning to ask. "You know ... when I was going from being in there," I pointed at the machine, "to being me?"

"Yeah," he admitted. "After the initial ... landing, which _was_ a little painful actually," he reminded me that I'd said I didn't think it would hurt, "it was stunning – _you_ were stunning. Everything glowed – the field, the grass, the sky, but especially you."

"Did you ... um," I ground to a halt, not knowing how to ask what I wanted to know.

"Did I hear any thoughts, find out any secrets, stuff like that?" John knew exactly what I was worried about. "Not so much," he reassured me. "It took pretty much all I had left after having to drag your lifeless body to that console just to build that bridge."

"You did good," I complemented him. "Once I'd got past your rickety ancient bridge," I teased, "I didn't even have to try – you pretty much drew me the rest of the way back by yourself."

"Yeah, well the first bit I just cobbled together quickly – it was pretty flimsy but you were already there before I could make it more solid," John took a few steps away from me, idly running a finger over one of the designs on the wall. "The second one wasn't any effort at all – I had it all there in my head."

He turned back to me and looked at me intently. "From day one I felt like I had to build on the connection we already had just to maintain my position with you. Every little thing I did to get closer to you ... was about trying to make that even stronger ... so you'd want to stay with me. So when you said bridge, it was that connection that I thought of and it just appeared like that, like I'd had it there the whole time."

"It was a beautiful bridge," I admitted, "the most beautiful bridge I'll ever see."

"Let's not go overboard here," John's face flushed a little in embarrassment. "I'm just ...," he took a deep steadying breath, "_glad_ that it worked so well."

We'd been on our feet for a while and I was still easily tired after my ordeal in that very room. When I took my customary seat on the floor with my back resting against the wall, John walked over and joined me, sitting close enough that our shoulders brushed if either of us moved.

"How are we doing?" he asked me after a few minutes of companionable silence. "You got any more anger issues before we move on to the gut spilling?"

"I thought we _were_ doing the gut spilling," I laughed.

"You think I'm gonna let you off that lightly?" John turned to look at me. "Think again."

"I _do_ have a question," I hesitated, wondering if I should bring it up. "When you were on your way to the jumper bay ... were you going to tell me what you were doing?"

"I don't know," John admitted. "I'm not that good at the whole 'last words' thing so whatever I said would have come out wrong anyway."

"You _do_ know!" I got up again to pace in front of him. "You had no intention of telling me anything! Just like when you snuck off to the Daedalus while I was in the infirmary."

"I didn't sneak!" John protested. "Look, in the military you can't always tell the people close to you what you're doing. Besides, there would have been no point in upsetting you before anything had even happened."

"Right, like finding out after and realising I never got to say goodbye would have been so much better!" I said hotly.

"I don't see what the problem is here," John complained, getting up and putting himself in my path.

"I _love_ you, you insensitive jerk!" I yelled up into his face. "It would have been nice to have been able to tell you once before you scattered yourself all over the atmosphere!"

"Well, it would have served you right, waiting until I was about to _die_ before telling me," John yelled back before we both realised what I'd admitted. "You love me," he confirmed with a smug grin. "I knew you did but I never thought you'd admit it ... nice delivery by the way."

"Yeah, well enjoy it because I probably won't be saying it too often," I turned away. "I might love you but you are a serious pain in the arse sometimes!"

"What a thing to say about the man you love," John teased, grabbing my hands and pulling me towards him. "You're not alone," he said before wrapping me in his arms and kissing me senseless.

"Hey," I pulled away, putting my hands on his chest to hold him back. "You promised me gut spilling and _that's_ the best you can do?"

"I'm a _guy_," John almost whined. "We're not good at this kind of thing."

"_John!_" I warned. "If you want that make-up sex you mentioned you've gotta do better than that!"

"Okay, okay," John laughed and I realised he'd been teasing me. "I love you," he said it easily. "Have since that first running session when you busted yourself to keep up and never complained. I know I made mistakes, made you doubt me, but that never changed."

"Very nice," I smiled as I complemented his declaration, feeling almost embarrassed by his comfortable show of emotion. "Much better than mine."

"You just need practice," John said seriously.

"Maybe," I admitted. "Would it bother you if I never get comfortable with the whole expressing my emotions thing?"

"Nah, as long as you try once in a while," John pulled me close again and held me tightly to his chest. "Besides I've got to think about my image you know – can't have you gushing over me all day – no one would take me seriously!"

"Ha Ha," I hit his shoulder as hard as I could, making little impression. "Don't worry – I don't see girly gushing anywhere in your future."

"That's a relief," John muttered, planting kisses across my face as he pulled the right parts of our bodies into alignment. I shivered as John nuzzled his head into my neck, his hands already under my t-shirt.

"This doesn't mean I'm going to start obeying your orders," I gasped as John kissed his way up the side of my neck.

"I never for a moment thought it would," John denied before taking over my mouth with a heated kiss.

"Do you really want to be doing this here?" I broke away to ask breathlessly. John looked around as if just noticing for the first time that we were still in the Wraith weapon room.

"You're right," he agreed. "It's cold in here and I'm too old to be rolling around on a concrete floor." John grabbed my hand and dragged me out of the room. I had to run to keep up with his long strides as he quickly found the shortest path back to his quarters – luckily there was no one around to witness our mad dash, complete with crazy laughter.

Once we had the door of his quarters firmly closed behind us, we looked at each other steadily. It only took a few seconds to remember where we'd left off – John was right – it was warmer there and his bed was much better than a concrete floor. I didn't think I could feel any closer to him than I had the previous times we'd been intimate but somehow having spoken of our feelings made a difference. It was just as intense as before but it was also tender with less urgency and more stability – and it cemented within my mind the belief that he really did love me.

Gut spilling, anger management, and make-up sex – what more could anyone ask for? Oh right – the happily ever after – it was still early days but even that didn't seem like such a stretch any more.

Authors Note: Finished! I do have a sort of epilogue written but I also had vague thoughts of continuing this into Season Two. Any opinions? Thanks to those who reviewed - PinkBug and EmSyd - along the way. Hope you enjoyed the ending!


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